From: MorellThomas <morellth@yahoo.co.jp>
Date: Fri, 8 Sep 2023 08:47:04 +0000 (+0200)
Subject: Properly integrated endGaps option for AlignSeq.traceAlignment()
X-Git-Tag: Release_2_11_4_0~31^2~37
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6c36212c1e16557e6afb1b4dba9c28864d52ad4a;p=jalview.git

Properly integrated endGaps option for AlignSeq.traceAlignment()
---

diff --git a/build.gradle b/build.gradle
index a917a0d..800fe42 100644
--- a/build.gradle
+++ b/build.gradle
@@ -53,7 +53,6 @@ plugins {
   id 'eclipse'
   id "com.diffplug.spotless" version "6.18.0" //.gradle.spotless" "3.28.0"
   id 'com.github.johnrengelman.shadow' version '8.1.1'	// was 4.0.3
-  id "com.diffplug.gradle.spotless" version "3.28.0"
   id 'com.install4j.gradle' version '10.0.3'
   id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
   id 'com.palantir.git-version' version '0.13.0' apply false
@@ -194,7 +193,7 @@ ext {
   testDir = string("${jalviewDir}/${bareTestSourceDir}")
 
   classesDir = string("${jalviewDir}/${classes_dir}")
-  outputDir = file(classesDir)
+  destinationDirectory = file(classesDir)
 
   // clover
   useClover = clover.equals("true")
@@ -592,14 +591,14 @@ sourceSets {
   main {
     java {
       srcDirs sourceDir
-      outputDir = file(classesDir)
+      destinationDirectory = file(classesDir)
     }
 
     resources {
       srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    compileClasspath = files(sourceSets.main.java.outputDir)
+    compileClasspath = files(sourceSets.main.java.destinationDirectory)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -609,14 +608,14 @@ sourceSets {
   clover {
     java {
       srcDirs cloverInstrDir
-      outputDir = cloverClassesDir
+      destinationDirectory = cloverClassesDir
     }
 
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.clover.java.outputDir )
+    compileClasspath = files( sourceSets.clover.java.destinationDirectory )
     //compileClasspath += files( testClassesDir )
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
     compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
@@ -628,14 +627,14 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file(testClassesDir)
+      destinationDirectory = file(testClassesDir)
     }
 
     resources {
       srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.test.java.outputDir )
+    compileClasspath = files( sourceSets.test.java.destinationDirectory )
     compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
@@ -660,7 +659,7 @@ eclipse {
   }
 
   classpath {
-    //defaultOutputDir = sourceSets.main.java.outputDir
+    //defaultOutputDir = sourceSets.main.java.destinationDirectory
     configurations.each{ c->
       if (c.isCanBeResolved()) {
         minusConfigurations += [c]
@@ -699,7 +698,7 @@ eclipse {
         HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
 
         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
-          //don't want to add outputDir as eclipse is using its own output dir in bin/main
+          //don't want to add destinationDirectory as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath, especially if they don't exist
             return false // groovy "continue" in .any closure
@@ -719,7 +718,7 @@ eclipse {
         }
 
         sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
-          //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+          //no longer want to add destinationDirectory as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath
             return false // groovy "continue" in .any closure
@@ -1096,7 +1095,7 @@ compileTestJava {
 
 clean {
   doFirst {
-    delete sourceSets.main.java.outputDir
+    delete sourceSets.main.java.destinationDirectory
   }
 }
 
@@ -1104,7 +1103,7 @@ clean {
 cleanTest {
   dependsOn cleanClover
   doFirst {
-    delete sourceSets.test.java.outputDir
+    delete sourceSets.test.java.destinationDirectory
   }
 }
 
@@ -1196,7 +1195,7 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) {
 
 task copyDocs(type: Copy) {
   def inputDir = "${jalviewDir}/${doc_dir}"
-  def outputDir = "${docBuildDir}/${doc_dir}"
+  def destinationDirectory = "${docBuildDir}/${doc_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1217,10 +1216,10 @@ task copyDocs(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
@@ -1455,7 +1454,7 @@ def getMdSections(String content) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${helpBuildDir}/${help_dir}"
+  def destinationDirectory = "${helpBuildDir}/${help_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1480,11 +1479,11 @@ task copyHelp(type: Copy) {
     exclude('**/*.xml')
     exclude('**/*.jhm')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
   outputs.files(helpFile)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
@@ -1632,7 +1631,7 @@ task copyResources(type: Copy) {
   description = "Copy (and make text substitutions in) the resources dir to the build area"
 
   def inputDir = resourceDir
-  def outputDir = resourcesBuildDir
+  def destinationDirectory = resourcesBuildDir
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1653,10 +1652,10 @@ task copyResources(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 task copyChannelResources(type: Copy) {
@@ -1665,7 +1664,7 @@ task copyChannelResources(type: Copy) {
   description = "Copy the channel resources dir to the build resources area"
 
   def inputDir = "${channelDir}/${resource_dir}"
-  def outputDir = resourcesBuildDir
+  def destinationDirectory = resourcesBuildDir
   from(inputDir) {
     include(channel_props)
     filter(ReplaceTokens,
@@ -1679,10 +1678,10 @@ task copyChannelResources(type: Copy) {
   from(inputDir) {
     exclude(channel_props)
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 task createBuildProperties(type: WriteProperties) {
@@ -2085,8 +2084,8 @@ jar {
     "Implementation-Version": JALVIEW_VERSION
   }
 
-  def outputDir = "${jalviewDir}/${package_dir}"
-  outputDir = file(outputDir)
+  def destinationDirectory = "${jalviewDir}/${package_dir}"
+  destinationDirectory = file(destinationDirectory)
   archiveFileName = rootProject.name+".jar"
   duplicatesStrategy "EXCLUDE"
 
@@ -2097,11 +2096,11 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir(sourceSets.main.java.outputDir)
+  inputs.dir(sourceSets.main.java.destinationDirectory)
   sourceSets.main.resources.srcDirs.each{ dir ->
     inputs.dir(dir)
   }
-  outputs.file("${outputDir}/${archiveFileName}")
+  outputs.file("${destinationDirectory}/${archiveFileName}")
 }
 
 
@@ -3331,10 +3330,10 @@ task jalviewjsEclipseCopyDropins(type: Copy) {
 
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
   inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
-  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
 }
 
 
@@ -3442,13 +3441,13 @@ task jalviewjsSyncAllLibs (type: Sync) {
   dependsOn jalviewjsTransferUnzipAllLibs
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
   inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3467,13 +3466,13 @@ task jalviewjsSyncResources (type: Sync) {
   dependsOn buildResources
 
   def inputFiles = fileTree(dir: resourcesBuildDir)
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3486,13 +3485,13 @@ task jalviewjsSyncResources (type: Sync) {
 
 task jalviewjsSyncSiteResources (type: Sync) {
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3506,13 +3505,13 @@ task jalviewjsSyncSiteResources (type: Sync) {
 task jalviewjsSyncBuildProperties (type: Sync) {
   dependsOn createBuildProperties
   def inputFiles = [file(buildProperties)]
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3731,7 +3730,7 @@ task jalviewjsBuildAllCores {
   def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
   def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
   def prefixFile = "${jsDir}/core/coretop2.js"
   def suffixFile = "${jsDir}/core/corebottom2.js"
 
@@ -3775,8 +3774,8 @@ task jalviewjsBuildAllCores {
     }
     def list = fileTree(dir: j2sDir, includes: filelist)
 
-    def jsfile = "${outputDir}/core${name}.js"
-    def zjsfile = "${outputDir}/core${name}.z.js"
+    def jsfile = "${destinationDirectory}/core${name}.js"
+    def zjsfile = "${destinationDirectory}/core${name}.z.js"
 
     jalviewjsCoreClasslists += [
       'jsfile': jsfile,
@@ -3794,8 +3793,8 @@ task jalviewjsBuildAllCores {
   // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
   def stevesoftClasslistName = "_stevesoft"
   def stevesoftClasslist = [
-    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
-    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js",
     'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
     'name': stevesoftClasslistName
   ]
@@ -3828,8 +3827,8 @@ task jalviewjsBuildAllCores {
     ]
   )
   def allClasslist = [
-    'jsfile': "${outputDir}/core${allClasslistName}.js",
-    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${allClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js",
     'list': allJsFiles,
     'name': allClasslistName
   ]
@@ -3882,11 +3881,11 @@ task jalviewjsPublishCoreTemplates {
   dependsOn jalviewjsBuildAllCores
   def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
   def inputFile = file(inputFileName)
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
 
   def outputFiles = []
   jalviewjsCoreClasslists.each { cl ->
-    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+    def outputFile = "${destinationDirectory}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
     cl['outputfile'] = outputFile
     outputFiles += outputFile
   }
@@ -3905,13 +3904,13 @@ task jalviewjsSyncCore (type: Sync) {
   dependsOn jalviewjsBuildAllCores
   dependsOn jalviewjsPublishCoreTemplates
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3448e79..4ec0457 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -381,7 +381,6 @@ public class AlignSeq
   /**
    * DOCUMENT ME!
    */
-  //&! not / 10
   public void traceAlignment()
   {
     // Find the maximum score along the rhs or bottom row
@@ -411,7 +410,103 @@ public class AlignSeq
     int j = maxj;
     int trace;
     maxscore = score[i][j] / 10f;
-    //maxscore = score[i][j];
+
+
+    aseq1 = new int[seq1.length + seq2.length];
+    aseq2 = new int[seq1.length + seq2.length];
+
+    StringBuilder sb1 = new StringBuilder(aseq1.length);
+    StringBuilder sb2 = new StringBuilder(aseq2.length);
+
+    count = (seq1.length + seq2.length) - 1;
+
+
+    while (i > 0 && j > 0)
+    {
+      aseq1[count] = seq1[i];
+      sb1.append(s1str.charAt(i));
+      aseq2[count] = seq2[j];
+      sb2.append(s2str.charAt(j));
+
+      trace = findTrace(i, j);
+
+      if (trace == 0)
+      {
+        i--;
+        j--;
+      }
+      else if (trace == 1)
+      {
+        j--;
+        aseq1[count] = GAP_INDEX;
+        sb1.replace(sb1.length() - 1, sb1.length(), "-");
+      }
+      else if (trace == -1)
+      {
+        i--;
+        aseq2[count] = GAP_INDEX;
+        sb2.replace(sb2.length() - 1, sb2.length(), "-");
+      }
+
+      count--;
+    }
+
+    seq1start = i + 1;
+    seq2start = j + 1;
+
+    if (aseq1[count] != GAP_INDEX)
+    {
+      aseq1[count] = seq1[i];
+      sb1.append(s1str.charAt(i));
+    }
+
+    if (aseq2[count] != GAP_INDEX)
+    {
+      aseq2[count] = seq2[j];
+      sb2.append(s2str.charAt(j));
+    }
+
+
+    /*
+     * we built the character strings backwards, so now
+     * reverse them to convert to sequence strings
+     */
+    astr1 = sb1.reverse().toString();
+    astr2 = sb2.reverse().toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void traceAlignmentWithEndGaps()
+  {
+    // Find the maximum score along the rhs or bottom row
+    float max = -Float.MAX_VALUE;
+
+    for (int i = 0; i < seq1.length; i++)
+    {
+      if (score[i][seq2.length - 1] > max)
+      {
+        max = score[i][seq2.length - 1];
+        maxi = i;
+        maxj = seq2.length - 1;
+      }
+    }
+
+    for (int j = 0; j < seq2.length; j++)
+    {
+      if (score[seq1.length - 1][j] > max)
+      {
+        max = score[seq1.length - 1][j];
+        maxi = seq1.length - 1;
+        maxj = j;
+      }
+    }
+
+    int i = maxi;
+    int j = maxj;
+    int trace;
+    maxscore = score[i][j] / 10f;
 
     //&! get trailing gaps
     while ((i < seq1.length - 1) || (j < seq2.length - 1))
@@ -658,14 +753,12 @@ public class AlignSeq
    * 
    * @return DOCUMENT ME!
    */
-  //&! not * 10
   public int findTrace(int i, int j)
   {
     int t = 0;
     float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
             s2str.charAt(j));
     float max = score[i - 1][j - 1] + (pairwiseScore * 10);
-    //float max = score[i - 1][j - 1] + (pairwiseScore);
 
     if (F[i][j] > max)
     {
@@ -703,7 +796,6 @@ public class AlignSeq
   /**
    * DOCUMENT ME!
    */
-  //&! not * 10
   public void calcScoreMatrix()
   {
     int n = seq1.length;
@@ -711,7 +803,6 @@ public class AlignSeq
 
     // top left hand element
     score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
-            //s2str.charAt(0));
             s2str.charAt(0)) * 10;
     E[0][0] = -GAP_EXTEND_COST;
     F[0][0] = 0;
@@ -727,7 +818,6 @@ public class AlignSeq
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
               s2str.charAt(j));
       score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST,
-      //score[0][j] = max(pairwiseScore, -GAP_OPEN_COST,
               -GAP_EXTEND_COST);
 
       traceback[0][j] = 1;
@@ -743,7 +833,6 @@ public class AlignSeq
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
               s2str.charAt(0));
       score[i][0] = max(pairwiseScore * 10, E[i][0], F[i][0]);
-      //score[i][0] = max(pairwiseScore, E[i][0], F[i][0]);
       traceback[i][0] = -1;
     }
 
@@ -760,7 +849,6 @@ public class AlignSeq
         float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
                 s2str.charAt(j));
         score[i][j] = max(score[i - 1][j - 1] + (pairwiseScore * 10),
-        //score[i][j] = max(score[i - 1][j - 1] + (pairwiseScore),
                 E[i][j], F[i][j]);
         traceback[i][j] = findTrace(i, j);
       }
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 21fa2f1..c84c69a 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -606,7 +606,8 @@ public class Finder implements FinderI
     }
     else
     {
-      allFeatures = sf.getAllFeatures(null);
+      //allFeatures = sf.getAllFeatures(null);
+      allFeatures = sf.getAllFeatures();
     }
     // so we can check we are advancing when debugging
     long fpos = 0;
diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index e9236cb..77c28be 100755
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -241,7 +241,7 @@ public class PaSiMap implements Runnable
     {
       // run needleman regardless if aligned or not
       // gui.PairwiseAlignPanel <++>
-      PairwiseAlignPanel alignment = new PairwiseAlignPanel(seqs);
+      PairwiseAlignPanel alignment = new PairwiseAlignPanel(seqs, true);
       float[][] scores = alignment.getAlignmentScores();	//bigger index first -- eg scores[14][13]
 
       Hashtable<SequenceI, Integer> connectivity = seqs.calculateConnectivity(scores, dim);
diff --git a/src/jalview/analysis/ccAnalysis.java b/src/jalview/analysis/ccAnalysis.java
index 948aa8f..5e149b8 100755
--- a/src/jalview/analysis/ccAnalysis.java
+++ b/src/jalview/analysis/ccAnalysis.java
@@ -792,6 +792,7 @@ public class ccAnalysis
 
   /**
   * check the termination condition for nonlinear least squares
+  * TODO can be removed and added just as one line in trf (: terminationStatus = (ftolSatisfied condition || xtolSatisfied condition) ? 1 : 0;)  doesnt matter as long as distinguished between 0 and rest
   *
   * @param actualReduction
   * @param cost
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 8b2a5c3..e6604d1 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1106,7 +1106,6 @@ public class AlignmentView
           }
         }
       }
-      //&!
       AlignmentI visal = view.getVisibleAlignment('-');
       if (visal != null)
       {
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 49bd4e9..3deb8e0 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3787,7 +3787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(new PairwiseAlignPanel(viewport));
+      frame.setContentPane(new PairwiseAlignPanel(viewport, false));
       Desktop.addInternalFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,
               500);
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 816b537..6a3aa0b 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -89,7 +89,7 @@ public class CalculationChooser extends JPanel
 
   private static final int MIN_PCA_SELECTION = 4;
 
-  private static final int MIN_PASIMAP_SELECTION = 4; //&! <++>!! chekc how many
+  private static final int MIN_PASIMAP_SELECTION = 8; //&!
 
   AlignFrame af;
 
diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index 62a0c80..f3a1f52 100644
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -109,8 +109,8 @@ public class PaSiMapPanel extends GPCAPanel
 
     boolean selected = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 0;
-    //&! do i need seqstrings?
-    AlignmentView seqstrings = av.getAlignmentView(selected);
+    //&! do i need seqstrings? -> no
+    //AlignmentView seqstrings = av.getAlignmentView(selected);
     SequenceI[] seqs;
     if (!selected)
     {
@@ -420,7 +420,7 @@ public class PaSiMapPanel extends GPCAPanel
     }
   }
 
-  public void makePaSiMapImage(ImageMaker.TYPE type)
+  public void makePaSiMapImage(ImageMaker.TYPE type)  throws Exception
   {
     int width = getRotatableCanvas().getWidth();
     int height = getRotatableCanvas().getHeight();
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 1cca215..e51024e 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -57,7 +57,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * @param viewport
    *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignmentViewport viewport)
+  public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps)
   {
     super();
     this.av = viewport;
@@ -107,7 +107,14 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         }
 
         as.calcScoreMatrix();
-        as.traceAlignment();
+	if (endGaps)
+	{
+	  //&!
+          as.traceAlignmentWithEndGaps();
+	} else {
+	  as.traceAlignment();
+	}
+	//&!
 	as.scoreAlignment();
 
         if (!first)
@@ -118,8 +125,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         first = false;
         as.printAlignment(System.out);
         scores[i][j] = as.getMaxScore() / as.getASeq1().length;
-        alignmentScores[i][j] = as.getAlignmentScore();
 	//&!
+        alignmentScores[i][j] = as.getAlignmentScore();
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
diff --git a/test/jalview/gui/PairwiseAlignmentPanelTest.java b/test/jalview/gui/PairwiseAlignmentPanelTest.java
index 750698a..34e5877 100644
--- a/test/jalview/gui/PairwiseAlignmentPanelTest.java
+++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java
@@ -55,7 +55,7 @@ public class PairwiseAlignmentPanelTest
     sg.setEndRes(35);
     viewport.setSelectionGroup(sg);
 
-    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
+    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport, false);
 
     String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
     String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
@@ -80,7 +80,7 @@ public class PairwiseAlignmentPanelTest
             DataSourceType.PASTE);
     AlignViewport viewport = af.getViewport();
 
-    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
+    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport, false);
 
     String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
     String expected = "Score = 80.0\n" + "Length of alignment = 4\n"