sequences are private in SequenceGroup

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 93f48ee..495469c 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -647,13 +647,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
       {\r
         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-        if (!sg.sequences.contains(seq))\r
+        if (!sg.getSequences(false).contains(seq))\r
         {\r
           continue;\r
         }\r
 \r
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
-        if (sg.sequences.contains(temp))\r
+        if (sg.getSequences(false).contains(temp))\r
         {\r
           continue;\r
         }\r
@@ -667,13 +667,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
       {\r
         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-        if (!sg.sequences.contains(seq))\r
+        if (!sg.getSequences(true).contains(seq))\r
         {\r
           continue;\r
         }\r
 \r
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
-        if (sg.sequences.contains(temp))\r
+        if (sg.getSequences(true).contains(temp))\r
         {\r
           continue;\r
         }\r
@@ -697,7 +697,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceGroup sg = viewport.getSelectionGroup();\r
     copiedSequences = new StringBuffer();\r
     Hashtable orderedSeqs = new Hashtable();\r
-    for (int i = 0; i < sg.getSize(); i++)\r
+    for (int i = 0; i < sg.getSize(false); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
       int index = viewport.alignment.findIndex(seq);\r
@@ -707,7 +707,7 @@ public void itemStateChanged(ItemEvent evt)
     int index = 0, startRes, endRes;\r
     char ch;\r
 \r
-    for (int i = 0; i < sg.getSize(); i++)\r
+    for (int i = 0; i < sg.getSize(false); i++)\r
     {\r
         SequenceI seq = null;\r
 \r
@@ -853,10 +853,10 @@ public void itemStateChanged(ItemEvent evt)
 \r
     SequenceGroup sg = viewport.getSelectionGroup();\r
     boolean allSequences = false;\r
-    if(sg.sequences.size()==viewport.alignment.getHeight())\r
+    if(sg.getSize(false)==viewport.alignment.getHeight())\r
           allSequences = true;\r
 \r
-    for (int i = 0; i < sg.sequences.size(); i++)\r
+    for (int i = 0; i < sg.getSize(false); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
       int index = viewport.getAlignment().findIndex(seq);\r
@@ -1037,10 +1037,10 @@ public void itemStateChanged(ItemEvent evt)
     int start=0, end = viewport.alignment.getWidth();\r
 \r
     if (viewport.getSelectionGroup() != null\r
-        && viewport.getSelectionGroup().sequences != null\r
-        && viewport.getSelectionGroup().sequences.size()>0)\r
+        && viewport.getSelectionGroup().getSequences(false) != null\r
+        && viewport.getSelectionGroup().getSize(false)>0)\r
     {\r
-      seqs = viewport.getSelectionGroup().sequences;\r
+      seqs = viewport.getSelectionGroup().getSequences(true);\r
       start = viewport.getSelectionGroup().getStartRes();\r
       end = viewport.getSelectionGroup().getEndRes()+1;\r
     }\r
@@ -1146,7 +1146,8 @@ public void itemStateChanged(ItemEvent evt)
       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
       {\r
-        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+        ((ClustalxColourScheme)sg.cs).resetClustalX(\r
+            sg.getSequences(true), sg.getWidth());\r
       }\r
       sg.recalcConservation();\r
     }\r
@@ -1382,7 +1383,7 @@ public void itemStateChanged(ItemEvent evt)
         }\r
         if (cs instanceof ClustalxColourScheme)\r
         {\r
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+          sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
         }\r
         else\r
         {\r
@@ -1402,7 +1403,7 @@ public void itemStateChanged(ItemEvent evt)
             || cs instanceof Blosum62ColourScheme)\r
         {\r
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+          sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
         }\r
         else\r
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
@@ -1411,7 +1412,7 @@ public void itemStateChanged(ItemEvent evt)
         {\r
           Conservation c = new Conservation("Group",\r
                                             ResidueProperties.propHash, 3,\r
-                                            sg.sequences, 0,\r
+                                            sg.getSequences(true), 0,\r
                                             viewport.alignment.getWidth() - 1);\r
           c.calculate();\r
           c.verdict(false, viewport.ConsPercGaps);\r
@@ -1529,7 +1530,7 @@ public void itemStateChanged(ItemEvent evt)
 \r
   public void pairwiseAlignmentMenuItem_actionPerformed()\r
   {\r
-    if (viewport.getSelectionGroup().getSize() > 1)\r
+    if (viewport.getSelectionGroup().getSize(false) > 1)\r
     {\r
       Frame frame = new Frame();\r
       frame.add(new PairwiseAlignPanel(alignPanel));\r
@@ -1559,8 +1560,8 @@ public void itemStateChanged(ItemEvent evt)
     }\r
 \r
     if ( (viewport.getSelectionGroup() != null &&\r
-          viewport.getSelectionGroup().getSize() < 4 &&\r
-          viewport.getSelectionGroup().getSize() > 0)\r
+          viewport.getSelectionGroup().getSize(false) < 4 &&\r
+          viewport.getSelectionGroup().getSize(false) > 0)\r
         || viewport.getAlignment().getHeight() < 4)\r
     {\r
       return;\r
@@ -1620,9 +1621,11 @@ public void itemStateChanged(ItemEvent evt)
 \r
     final TreePanel tp;\r
     if (viewport.getSelectionGroup() != null &&\r
-        viewport.getSelectionGroup().getSize() > 3)\r
+        viewport.getSelectionGroup().getSize(false) > 3)\r
     {\r
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
+      tp = new TreePanel(viewport,\r
+                         viewport.getSelectionGroup().getSequences(false),\r
+                         type,\r
                          pwType,\r
                          0, viewport.alignment.getWidth());\r
     }\r