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Create Multiple Alignment GUI
Analogously as with the pairwise alignments, now it is possible to trigger a multiple structure alignment throw a GUI where the input is made via a JTextField. Any numnber of structures can be analyzed. biojava#281 This required some new classes and the modification of some of the old ones.
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‎biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -66,9 +66,9 @@ public static void main(String[] args) throws IOException, StructureException, I
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}
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//Here the multiple structural alignment algorithm comes in place to generate the alignment object
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MultipleMcMain algorithm = new MultipleMcMain();
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MultipleMcMain algorithm = new MultipleMcMain(new CeCPMain());
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MultipleMcParameters params = (MultipleMcParameters) algorithm.getParameters();
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params.setPairwiseAlgorithm(CeCPMain.algorithmName);
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params.setMinBlockLen(10);
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MultipleAlignment result = algorithm.align(atomArrays);
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result.getEnsemble().setStructureNames(names);

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java‎

Lines changed: 2 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,6 @@
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*/
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package org.biojava.nbio.structure.align.gui;
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25-
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.StructureAlignment;
@@ -43,7 +42,6 @@
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import java.awt.event.ActionEvent;
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import java.io.File;
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/** A JFrame that allows to trigger a pairwise structure alignment,
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* either from files in a directory,
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* or after manual upload.
@@ -323,10 +321,9 @@ public void actionPerformed(ActionEvent evt) {
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protected void configureParameters() {
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StructureAlignment algorithm = getStructureAlignment();
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System.out.println("configure parameters for " + algorithm.getAlgorithmName());
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// show a new config GUI
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new ParameterGUI(algorithm);
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new ParameterGUI(algorithm.getParameters(), algorithm.getAlgorithmName());
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}
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‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java‎

Lines changed: 16 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,6 @@
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import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
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import org.biojava.nbio.structure.align.model.AFPChain;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.util.UserConfiguration;
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import org.biojava.nbio.structure.align.webstart.WebStartMain;
3029

@@ -122,6 +121,7 @@ public static JMenuBar initJmolMenu(JFrame frame, AbstractAlignmentJmol parent,
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//Exit
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JMenuItem exitI = getExitMenuItem();
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file.add(exitI);
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menu.add(file);
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/// ALIGN MENU
@@ -130,7 +130,10 @@ public static JMenuBar initJmolMenu(JFrame frame, AbstractAlignmentJmol parent,
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//new Pairwise alignment
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JMenuItem pairI = getPairwiseAlignmentMenuItem();
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align.add(pairI);
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//new Multiple alignment TODO
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//new Multiple alignment
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JMenuItem multI = getMultipleAlignmentMenuItem();
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align.add(multI);
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menu.add(align);
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/// VIEW MENU
@@ -626,13 +629,21 @@ public void actionPerformed(ActionEvent e) {
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}
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629-
/** provide a display for the pairwise structure alignment
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*
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/**
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* Provide a display for the pairwise structure alignment.
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*/
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private static void showPairDialog(){
633636
AlignmentGui gui = AlignmentGui.getInstance();
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gui.setVisible(true);
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}
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/**
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* Provide a display for the multiple structure alignment.
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*/
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private static void showMultipleDialog(){
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MultipleAlignmentGUI gui = MultipleAlignmentGUI.getInstance();
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gui.setVisible(true);
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}
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637648
/**
638649
* Show some info about this GUI
@@ -705,7 +716,7 @@ public void actionPerformed(ActionEvent e) {
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String cmd = e.getActionCommand();
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707718
if ( cmd.equals(MULTIPLE_ALIGN)){
708-
MenuCreator.showPairDialog();
719+
MenuCreator.showMultipleDialog();
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}
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}
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});

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java‎

Lines changed: 118 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,118 @@
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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
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* be distributed with the code. If you do not have a copy,
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* see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
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* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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* Created on Jul 16, 2006
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*
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*/
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package org.biojava.nbio.structure.align.gui;
24+
25+
import java.util.ArrayList;
26+
import java.util.List;
27+
28+
import org.biojava.nbio.structure.Atom;
29+
import org.biojava.nbio.structure.Structure;
30+
import org.biojava.nbio.structure.StructureException;
31+
import org.biojava.nbio.structure.StructureTools;
32+
import org.biojava.nbio.structure.align.MultipleStructureAligner;
33+
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
34+
import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
36+
37+
/**
38+
* A class that obtains structures via DAS and aligns them.
39+
* This is done in a separate thread.
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* It is possible to register Event listeners to get notification of when
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* the download has finished.
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*
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* @author Aleix Lafita
44+
* @since 4.1.1
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*
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*/
47+
public class MultipleAlignmentCalc implements AlignmentCalculationRunnable {
48+
49+
private static final Logger logger =
50+
LoggerFactory.getLogger(MultipleAlignmentCalc.class);
51+
52+
private boolean interrupted = false;
53+
private List<String> names;
54+
private List<Structure> structures;
55+
56+
private MultipleAlignmentGUI parent;
57+
58+
/**
59+
* Requests an alignment of the pdbs.
60+
* If they are empty strings, they are ignored.
61+
*
62+
* @param parent the gui frame that interacts with this class
63+
* @param structures
64+
* @param names
65+
*/
66+
public MultipleAlignmentCalc(MultipleAlignmentGUI parent,
67+
List<Structure> structures, List<String> names) {
68+
69+
this.parent= parent;
70+
this.structures = structures;
71+
this.names = names;
72+
}
73+
74+
@Override
75+
public void run() {
76+
77+
MultipleStructureAligner algorithm =
78+
parent.getMultipleStructureAligner();
79+
try {
80+
81+
List<Atom[]> atomArrays = new ArrayList<Atom[]>();
82+
for (Structure s:structures){
83+
Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
84+
atomArrays.add(ca);
85+
}
86+
87+
MultipleAlignment msa = algorithm.align(atomArrays);
88+
msa.getEnsemble().setStructureNames(names);
89+
90+
MultipleAlignmentDisplay.display(msa);
91+
92+
} catch (StructureException e) {
93+
e.printStackTrace();
94+
logger.warn(e.getMessage());
95+
}
96+
97+
parent.notifyCalcFinished();
98+
}
99+
100+
@Override
101+
public void interrupt() {
102+
interrupted = true;
103+
}
104+
105+
@Override
106+
public void cleanup() {
107+
108+
parent.notifyCalcFinished();
109+
parent=null;
110+
structures = null;
111+
names = null;
112+
}
113+
114+
@Override
115+
public void setNrCPUs(int useNrCPUs) {
116+
// TODO Auto-generated method stub
117+
}
118+
}

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