Now has res start, res end

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c8b375a..051db30 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -5,35 +5,40 @@ import jalview.analysis.*;
 import jalview.datamodel.*;\r
 import java.util.Vector;\r
 \r
-public class SequenceGroup{\r
-    String groupName;\r
-    boolean isSelected;\r
-    boolean displayBoxes;\r
-    boolean displayText;\r
-    boolean colourText;\r
-    boolean display;\r
-    Conservation conserve;\r
-    Vector   aaFrequency;\r
-    boolean     aaFrequencyValid = false;\r
-    public Vector sequences = new Vector();\r
-    int         width = -1;\r
-    public ColourSchemeI cs;\r
-\r
-\r
-  public SequenceGroup() {\r
+public class SequenceGroup\r
+{\r
+  String groupName;\r
+  boolean isSelected;\r
+  boolean displayBoxes;\r
+  boolean displayText;\r
+  boolean colourText;\r
+  boolean display;\r
+  Conservation conserve;\r
+  Vector aaFrequency;\r
+  boolean aaFrequencyValid = false;\r
+  public Vector sequences = new Vector();\r
+  int width = -1;\r
+  public ColourSchemeI cs;\r
+  int startRes = 20;\r
+  int endRes = 35;\r
+\r
+  public SequenceGroup()\r
+  {\r
     groupName = "Group";\r
     this.isSelected = false;\r
     this.displayBoxes = true;\r
     this.displayText = true;\r
     this.colourText = false;\r
     this.display = true;\r
-    cs = new ZappoColourScheme();\r
+    cs = null;\r
   }\r
 \r
-  public SequenceGroup( String groupName, ColourSchemeI scheme, boolean isSelected,\r
-                        boolean displayBoxes, boolean displayText,\r
-                        boolean colourText,\r
-                        boolean display) {\r
+  public SequenceGroup(String groupName, ColourSchemeI scheme,\r
+                       boolean isSelected,\r
+                       boolean displayBoxes, boolean displayText,\r
+                       boolean colourText,\r
+                       boolean display)\r
+  {\r
 \r
     this.groupName = groupName;\r
     this.isSelected = isSelected;\r
@@ -53,69 +58,107 @@ public class SequenceGroup{
   {\r
     groupName = name;\r
   }\r
-  public Conservation getConservation() {\r
-     return conserve;\r
+\r
+  public Conservation getConservation()\r
+  {\r
+    return conserve;\r
   }\r
+\r
   public void setConservation(Conservation c)\r
-  { conserve = c; }\r
+  {\r
+    conserve = c;\r
+  }\r
 \r
-  public void addSequence(SequenceI s) {\r
+  public void addSequence(SequenceI s)\r
+  {\r
     sequences.addElement(s);\r
   }\r
 \r
-  public void deleteSequence(SequenceI s) {\r
+  public void deleteSequence(SequenceI s)\r
+  {\r
     sequences.removeElement(s);\r
   }\r
 \r
-  public void setColourText(boolean state) {\r
+  public void setColourText(boolean state)\r
+  {\r
     colourText = state;\r
   }\r
-  public boolean getColourText() {\r
+\r
+  public boolean getColourText()\r
+  {\r
     return colourText;\r
   }\r
 \r
-  public void setDisplayText(boolean state) {\r
+  public void setDisplayText(boolean state)\r
+  {\r
     displayText = state;\r
   }\r
 \r
-  public boolean getDisplayText() {\r
+  public boolean getDisplayText()\r
+  {\r
     return displayText;\r
   }\r
 \r
-  public void setDisplayBoxes(boolean state) {\r
+  public void setDisplayBoxes(boolean state)\r
+  {\r
     displayBoxes = state;\r
   }\r
 \r
-  public boolean getDisplayBoxes() {\r
+  public boolean getDisplayBoxes()\r
+  {\r
     return displayBoxes;\r
   }\r
 \r
-    public int getSize() {\r
-       return sequences.size();\r
-    }\r
-    public SequenceI  getSequenceAt(int i) {\r
-       return (SequenceI)sequences.elementAt(i);\r
-    }\r
+  public int getStartRes()\r
+  {\r
+    return startRes;\r
+  }\r
+\r
+  public int getEndRes()\r
+  {\r
+    return endRes;\r
+  }\r
+\r
+  public void setStartRes(int i)\r
+  {\r
+    startRes = i;\r
+  }\r
+\r
+  public void setEndRes(int i)\r
+  {\r
+    endRes = i;\r
+  }\r
+\r
+  public int getSize()\r
+  {\r
+    return sequences.size();\r
+  }\r
 \r
-    public Vector getAAFrequency() {\r
-       if (aaFrequency == null || aaFrequencyValid == false) {\r
-           aaFrequency = AAFrequency.calculate(sequences,0,getWidth());\r
-           aaFrequencyValid = true;\r
-       }\r
-       return aaFrequency;\r
+  public SequenceI getSequenceAt(int i)\r
+  {\r
+    return (SequenceI) sequences.elementAt(i);\r
+  }\r
+\r
+  public Vector getAAFrequency()\r
+  {\r
+    if (aaFrequency == null || aaFrequencyValid == false)\r
+    {\r
+      aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());\r
+      aaFrequencyValid = true;\r
     }\r
+    return aaFrequency;\r
+  }\r
 \r
-    public int getWidth()\r
+  public int getWidth()\r
+  {\r
+    System.out.println("it is called");\r
+    // MC This needs to get reset when characters are inserted and deleted\r
+    for (int i = 0; i < sequences.size(); i++)\r
     {\r
-       // MC This needs to get reset when characters are inserted and deleted\r
-        for (int i = 0; i < sequences.size(); i++)\r
-        {\r
-          SequenceI seq = (SequenceI) sequences.elementAt(i);\r
-          if (seq.getLength() > width)\r
-            width = seq.getLength();\r
-        }\r
-       return width;\r
+      SequenceI seq = (SequenceI) sequences.elementAt(i);\r
+      if (seq.getLength() > width)\r
+        width = seq.getLength();\r
     }\r
+    return width;\r
+  }\r
 }\r
-\r
-\r