Comments and credits.

paolopavan · unknown · commit 8026d8f5d7e4 · 2015-09-09T15:01:51.000+02:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hit.java
@@ -1,19 +1,20 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package org.biojava.nbio.core.search.io;
 
 import java.util.Iterator;
 import java.util.List;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- *
- * @author pavanpa
+ * This class models a search Hit.
+ * You will retrieve a list of this using iterator of a Result
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
  */
+
 public abstract class Hit implements Iterable<Hsp>{
     private final int hitNum;
     private final String hitId;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
@@ -1,9 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package org.biojava.nbio.core.search.io;
 
 import java.util.ArrayList;
@@ -24,9 +18,17 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- *
- * @author pavanpa
+ * This class models a search Hsp.
+ * You will retrieve a list of this using iterator of a Hit
+ * 
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
  */
+
 public abstract class Hsp <S extends Sequence<C>, C extends Compound> {
     private Integer hspNum;
     private Double hspBitScore;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Result.java
@@ -1,9 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package org.biojava.nbio.core.search.io;
 
 import java.util.HashMap;
@@ -13,10 +7,17 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- *  This class models a search result.
+ * This class models a search result.
  * You will find one of this for every query sequence specified in the run.
- * @author pavanpa
+ * 
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
  */
+
 public abstract class Result implements Iterable<Hit>{
     private String program;
     private String version;
@@ -116,7 +117,7 @@ public String getProgramSpecificParameter(String key) {
         return programSpecificParameters.get(key);
     }
     /**
-     * returns the reference th the original and whole sequence used to query the database.
+     * returns the reference to the original and whole sequence used to query the database.
      * Available only if the ResultFactory implements setQueryReferences and
      * it was used before the parsing with SearchIO
      * @return Sequence object
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
@@ -1,17 +1,17 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.biojava.nbio.core.search.io;
 
 import java.io.File;
 import java.util.List;
 
 /**
- *
- * @author pavanpa
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
  */
+
 public interface ResultFactory {
     /**
      * returns a list of file extensions associated to this ResultFactory
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
@@ -1,9 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package org.biojava.nbio.core.search.io;
 
 import java.io.File;
@@ -13,9 +7,14 @@
 import java.util.ServiceLoader;
 
 /**
- *
- * @author pavanpa
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
  */
+
 public class SearchIO implements Iterable<Result>{
     static private HashMap<String,ResultFactory> extensionFactoryAssociation;
     
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHitBuilder.java
@@ -1,16 +1,18 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.biojava.nbio.core.search.io.blast;
 
 
 import org.biojava.nbio.core.search.io.Hsp;
 import java.util.List;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
-
+/**
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
+ */
 public class BlastHitBuilder {
     private int hitNum;
     private String hitId;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHspBuilder.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastHspBuilder.java
@@ -1,10 +1,13 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.biojava.nbio.core.search.io.blast;
 
+/**
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
+ */
 
 public class BlastHspBuilder {
     private int hspNum;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResult.java
@@ -1,9 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package org.biojava.nbio.core.search.io.blast;
 
 import org.biojava.nbio.core.search.io.Hit;
@@ -13,9 +7,16 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- *  This class models a Blast/Blast plus result.
+ * This class models a Blast/Blast plus result.
  * You will find one of this for every query sequence specified in the run.
- * @author pavanpa
+ * 
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
+ * 
  */
 public class BlastResult extends Result{
     public BlastResult(String program, String version, String reference, String dbFile, HashMap<String, String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastResultBuilder.java
@@ -1,16 +1,18 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package org.biojava.nbio.core.search.io.blast;
 
 import org.biojava.nbio.core.search.io.Hit;
 import java.util.HashMap;
 import java.util.List;
 import org.biojava.nbio.core.sequence.template.Sequence;
 
+/**
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
+ */
 
 public class BlastResultBuilder {
     private String program;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java
@@ -1,9 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package org.biojava.nbio.core.search.io.blast;
 
 import java.io.File;
@@ -22,10 +16,14 @@
 import org.biojava.nbio.core.search.io.ResultFactory;
 
 /**
- *
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
  * @author Paolo Pavan
- * https://it.linkedin.com/pub/paolo-pavan/6/15a/956
  */
+
 public class BlastTabularParser implements ResultFactory {
     private final String blastReference = 
             "Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), A greedy algorithm for aligning DNA sequences&quot;, J Comput Biol 2000; 7(1-2):203-14.";
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLQuery.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLQuery.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.biojava.nbio.core.search.io.blast;
 
 
@@ -22,9 +18,13 @@
 import org.biojava.nbio.core.util.XMLHelper;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
-import org.xml.sax.SAXException;
 
 /**
+ * Re-designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
  *
  * @author Scooter Willis <willishf at gmail dot com>
  * @author Paolo Pavan
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/HspTest.java
@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.biojava.nbio.core.search.io;
 
 import org.biojava.nbio.alignment.template.SequencePair;
@@ -15,12 +10,16 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import static org.junit.Assert.*;
-import org.junit.Ignore;
 
 /**
- *
- * @author pavanpa
+ * Designed by Paolo Pavan.
+ * You may want to find my contacts on Github and LinkedIn for code info 
+ * or discuss major changes.
+ * https://github.com/paolopavan
+ * 
+ * @author Paolo Pavan
  */
+
 public class HspTest {
     
     Hsp hspImpl = new BlastHspBuilder()
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
