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josemduartejosemduarte
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Cosmetics
1 parent dc00a25 commit afdb837

12 files changed

Lines changed: 84 additions & 206 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java‎

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/** This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
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/**
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* This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
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* as has been originally developed by I. Shindyalov and P.Bourne (1998).
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* The original CE paper is available from here: <a href="http://peds.oxfordjournals.org/cgi/content/short/11/9/739">http://peds.oxfordjournals.org/cgi/content/short/11/9/739</a>.
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*
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* This class is a pretty much exact 1:1 port from C, where I cared about exact reproduce of the CE results
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* and not about Java style.
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*
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* @author Andreas Prlic
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*
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*/
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public class CECalculator {

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java‎

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/** This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
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/**
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* This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
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* as has been originally developed by I. Shindyalov and P.Bourne (1998).
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* The original CE paper is available from here: <a href="http://peds.oxfordjournals.org/cgi/content/short/11/9/739">http://peds.oxfordjournals.org/cgi/content/short/11/9/739</a>.
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*
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*
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* @author Spencer Bliven
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* @author Andreas Prlic
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*
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*
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*/
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public class CeCalculatorEnhanced {

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPParameters.java‎

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@@ -26,7 +26,8 @@
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import java.util.List;
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/** Contains the parameters that can be sent to CE
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/**
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* Contains the parameters that can be sent to CE
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*
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* @author Andreas Prlic
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*

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/StartupParameters.java‎

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@@ -21,15 +21,14 @@
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package org.biojava.nbio.structure.align.ce;
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/** a simple bean that contains the parameters that can get set at startup
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/**
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* A simple bean that contains the parameters that can get set at startup
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*
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* @author Andreas Prlic
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*
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*/
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public class StartupParameters {
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String pdbFilePath;
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String cacheFilePath;
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String outFile;

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/PdbPair.java‎

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@@ -24,10 +24,9 @@
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/**
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* A pair for structure alignment
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*
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* @author Andreas Prlic
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*
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* <p>
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* name1 is always < name2
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* @author Andreas Prlic
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*
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*/
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public class PdbPair implements Comparable<PdbPair> {

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java‎

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@@ -35,7 +35,8 @@
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import java.util.ArrayList;
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import java.util.List;
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/** a class that performs calculations on AFPCHains
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/**
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* A class that performs calculations on AFPChains
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*
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* @author Andreas Prlic
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*
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public static final boolean debug = FatCatAligner.debug;
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public static final void extractAFPChains(FatCatParameters params, AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws StructureException {
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public static void extractAFPChains(FatCatParameters params, AFPChain afpChain,Atom[] ca1,Atom[] ca2) throws StructureException {
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List<AFP> afpSet = new ArrayList<AFP>();
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afpChain.setAfpSet(afpSet);

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java‎

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public class FCAlignHelper
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{
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int M; //length of protein 1
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int N; //length of protein 2
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double g; //gap-create
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double h; //gap-extend
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double m; //g + h
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double[][] sij;
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char[][] trace; //trace-record
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char[][] etrace; //trace-record
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char[][] dtrace; //trace-record
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int B1; //beginning position of protein 1 in alignment
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int B2; //beginning position of protein 2 in alignment
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int E1; //end position of protein 1 in alignment
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int E2; //end position of protein 2 in alignment
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double alignScore;
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double identity;
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double similarity;
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int[] sapp;
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int[] sapp0;
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int sappPos;
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int last;
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char[] seq1;
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char[] seq2;
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char[] aln1;
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char[] aln2;
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char[] mark;
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/** do an alignment given the provided matrix sij0
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private int M; //length of protein 1
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private int N; //length of protein 2
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private double g; //gap-create
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private double h; //gap-extend
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private double m; //g + h
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private double[][] sij;
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private char[][] trace; //trace-record
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private char[][] etrace; //trace-record
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private char[][] dtrace; //trace-record
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private int B1; //beginning position of protein 1 in alignment
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private int B2; //beginning position of protein 2 in alignment
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private int E1; //end position of protein 1 in alignment
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private int E2; //end position of protein 2 in alignment
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private double alignScore;
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private double identity;
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private double similarity;
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private int[] sapp;
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private int[] sapp0;
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private int sappPos;
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private int last;
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private char[] seq1;
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private char[] seq2;
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private char[] aln1;
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private char[] aln2;
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private char[] mark;
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/**
60+
* do an alignment given the provided matrix sij0
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*
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* @param sij0 - the matrix to perform the calculations on.
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* @param M0

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java‎

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import java.util.List;
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/** A class that does calculations on an AFPChain
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/**
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* A class that does calculations on an AFPChain
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*
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* @author Andreas Prlic
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*

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java‎

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//private static final boolean showAlig = false;
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int pro1Len;
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int pro2Len;
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int maxLen;
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Atom[] cod1;
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Atom[] cod2;
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int[][] equSet;
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int equLen;
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int equLen0;
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double[][]sij;
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int maxKeepStep;
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int keepStep;
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double Dc; //the criteria for structural equivalent residues, eg. 3.0 (CE), 6.0(ProSup)
57-
double rmsdCut;//the criteria for stoping optimization
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double increase;
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double stopLenPer;
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double stopRmsdPer;
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double stopRmsd;
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double gapIni;
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double gapExt;
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double rmsd;
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private int pro1Len;
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private int pro2Len;
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private int maxLen;
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private Atom[] cod1;
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private Atom[] cod2;
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private int[][] equSet;
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private int equLen;
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private int equLen0;
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private double[][]sij;
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private int maxKeepStep;
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private int keepStep;
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private double Dc; //the criteria for structural equivalent residues, eg. 3.0 (CE), 6.0(ProSup)
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private double rmsdCut;//the criteria for stoping optimization
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private double increase;
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private double stopLenPer;
60+
private double stopRmsdPer;
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private double stopRmsd;
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63+
private double gapIni;
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private double gapExt;
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private double rmsd;
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private static final boolean debug = FatCatAligner.debug;
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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFP.java‎

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import java.io.Serializable;
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/** A class to represent a FATCAT AFP
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/**
28+
* A class to represent a FATCAT aligned fragment pair (AFP)
2829
*
2930
* @author Andreas Prlic
3031
*
3132
*/
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3333
public class AFP implements Serializable {
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35-
/**
36-
*
37-
*/
3835
private static final long serialVersionUID = 3901209995477111829L;
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int p1;
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int p2;
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int fragLen;
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double rmsd;
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Matrix m;
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double[] t;
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double score;
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47-
long id;
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private int p1;
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private int p2;
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private int fragLen;
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private double rmsd;
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private Matrix m;
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private double[] t;
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private double score;
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private long id;
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4947
@Override
50-
public String toString(){
48+
public String toString(){
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5250
// we use the metric of
53-
5451
// Manfred J. Sippl
5552
// On Distance and Similarity in Fold Space
5653
// Bioinformatics, 24, pp. 872-873 (2008)
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5955
StringBuffer buf = new StringBuffer();
6056
buf.append("AFP: p1:");
6157
buf.append(p1);
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this.score = score;
125121
}
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}

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