Remove left, right, empty cols work on hidden reps

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 90d6740..c0c4ae0 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -115,7 +115,6 @@ public class Alignment implements AlignmentI
         }\r
         else\r
         {\r
-          System.out.println("CLEARED HERE");\r
           Sequence ds = new Sequence(snew.getName(),\r
                                      AlignSeq.extractGaps("-. ",\r
               snew.getSequence()),\r
@@ -157,14 +156,26 @@ public class Alignment implements AlignmentI
      */\r
     public void removeGaps()\r
     {\r
+        SequenceI[] seqs = getVisibleAndRepresentedSeqs();\r
+        int j, jSize = seqs.length;\r
+\r
         SequenceI current;\r
-        int iSize = getWidth();\r
+        int width = 0;\r
+        for (int i = 0; i < jSize; i++)\r
+        {\r
+          if (seqs[i].getLength() > width)\r
+          {\r
+            width = seqs[i].getLength();\r
+          }\r
+        }\r
 \r
-        for (int i = 0; i < iSize; i++)\r
+        int startCol = -1, endCol = -1;\r
+        boolean delete = true;\r
+        for (int i = 0; i < width; i++)\r
         {\r
-            boolean delete = true;\r
+            delete = true;\r
 \r
-            for (int j = 0; j < getHeight(); j++)\r
+            for (j = 0; j < jSize; j++)\r
             {\r
                 current = getSequenceAt(j);\r
 \r
@@ -172,48 +183,51 @@ public class Alignment implements AlignmentI
                 {\r
                     if (!jalview.util.Comparison.isGap(current.getCharAt(i)))\r
                     {\r
+                        if(delete)\r
+                          endCol = i;\r
+\r
                         delete = false;\r
+                        break;\r
                     }\r
                 }\r
+\r
+            }\r
+\r
+            if(delete && startCol==-1)\r
+            {\r
+              startCol = i;\r
             }\r
 \r
-            if (delete)\r
+\r
+            if (!delete && startCol > -1)\r
             {\r
-                deleteColumns(i, i);\r
-                iSize--;\r
-                i--;\r
+              deleteColumns(seqs, startCol, endCol);\r
+              width -= (endCol - startCol);\r
+              i -= (endCol - startCol);\r
+              startCol = -1;\r
+              endCol = -1;\r
             }\r
         }\r
+\r
+        if (delete && startCol > -1)\r
+        {\r
+          deleteColumns(seqs, startCol, endCol);\r
+        }\r
+\r
     }\r
 \r
     /** Removes a range of columns (start to end inclusive).\r
      *\r
+     * @param seqs Sequences to remove columns from\r
      * @param start Start column in the alignment\r
      * @param end End column in the alignment\r
      */\r
-    public void deleteColumns(int start, int end)\r
+    public void deleteColumns(SequenceI [] seqs, int start, int end)\r
     {\r
-        deleteColumns(0, getHeight() - 1, start, end);\r
+      for(int i=0; i<seqs.length; i++)\r
+        seqs[i].deleteChars(start, end);\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param seq1 DOCUMENT ME!\r
-     * @param seq2 DOCUMENT ME!\r
-     * @param start DOCUMENT ME!\r
-     * @param end DOCUMENT ME!\r
-     */\r
-    public void deleteColumns(int seq1, int seq2, int start, int end)\r
-    {\r
-        for (int i = 0; i <= (end - start); i++)\r
-        {\r
-            for (int j = seq1; j <= seq2; j++)\r
-            {\r
-                getSequenceAt(j).deleteCharAt(start);\r
-            }\r
-        }\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -222,22 +236,22 @@ public class Alignment implements AlignmentI
      */\r
     public void trimLeft(int i)\r
     {\r
-        int j, jSize = getHeight();\r
+        SequenceI[] seqs = getVisibleAndRepresentedSeqs();\r
+        int j, jSize = seqs.length;\r
         for (j = 0; j < jSize; j++)\r
         {\r
-            SequenceI s = getSequenceAt(j);\r
-            int newstart = s.findPosition(i);\r
+            int newstart = seqs[j].findPosition(i);\r
 \r
-            if(i>s.getLength())\r
+            if(i>seqs[j].getLength())\r
             {\r
-              sequences.removeElement(s);\r
+              sequences.removeElement(seqs[j]);\r
               j--;\r
               jSize--;\r
             }\r
             else\r
             {\r
-              s.setStart(newstart);\r
-              s.setSequence(s.getSequence().substring(i));\r
+              seqs[j].setStart(newstart);\r
+              seqs[j].setSequence(seqs[j].getSequence().substring(i));\r
             }\r
         }\r
     }\r
@@ -249,14 +263,15 @@ public class Alignment implements AlignmentI
      */\r
     public void trimRight(int i)\r
     {\r
-        for (int j = 0; j < getHeight(); j++)\r
+        SequenceI[] seqs = getVisibleAndRepresentedSeqs();\r
+        int j, jSize = seqs.length;\r
+        for (j = 0; j < jSize; j++)\r
         {\r
-            SequenceI s = getSequenceAt(j);\r
-            int newend = s.findPosition(i);\r
+            int newend = seqs[j].findPosition(i);\r
 \r
-            s.setEnd(newend);\r
-            if(s.getLength()>i)\r
-              s.setSequence(s.getSequence().substring(0, i + 1));\r
+            seqs[j].setEnd(newend);\r
+            if(seqs[j].getLength()>i)\r
+              seqs[j].setSequence(seqs[j].getSequence().substring(0, i + 1));\r
         }\r
     }\r
 \r
@@ -744,4 +759,33 @@ public class Alignment implements AlignmentI
       return hiddenSequences;\r
     }\r
 \r
+    SequenceI [] getVisibleAndRepresentedSeqs()\r
+    {\r
+      if(hiddenSequences==null || hiddenSequences.getSize()<1)\r
+        return getSequencesArray();\r
+\r
+      Vector seqs = new Vector();\r
+      SequenceI seq;\r
+      SequenceGroup hidden;\r
+      for (int i = 0; i < sequences.size(); i++)\r
+      {\r
+        seq = (SequenceI) sequences.elementAt(i);\r
+        seqs.addElement(seq);\r
+        hidden = seq.getHiddenSequences();\r
+        if(hidden!=null)\r
+        {\r
+          for(int j=0; j<hidden.getSize(false); j++)\r
+          {\r
+            seqs.addElement(hidden.getSequenceAt(j));\r
+          }\r
+        }\r
+      }\r
+      SequenceI [] result = new SequenceI[seqs.size()];\r
+      for(int i=0; i<seqs.size(); i++)\r
+        result[i] = (SequenceI)seqs.elementAt(i);\r
+\r
+      return result;\r
+\r
+    }\r
+\r
 }\r

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index dbf3c35..e62c8c2 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -111,17 +111,8 @@ public interface AlignmentI
      * @param start Start index of columns to delete.\r
      * @param end End index to columns to delete.\r
      */\r
-    public void deleteColumns(int start, int end);\r
+    public void deleteColumns(SequenceI seqs [], int start, int end);\r
 \r
-    /**\r
-     * Deletes all residues in every sequence of alignment within given columns.\r
-     *\r
-     * @param seq1 Index of first sequence to delete columns from.\r
-     * @param seq2 Index of last sequence to delete columns from.\r
-     * @param start Start index of columns to delete.\r
-     * @param end End index of columns to delete.\r
-     */\r
-    public void deleteColumns(int seq1, int seq2, int start, int end);\r
 \r
     /**\r
      * Finds sequence in alignment using sequence name as query.\r