group has outline colour

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6bccec3..4c6420c 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -4,49 +4,47 @@ import jalview.schemes.*;
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 import java.util.Vector;\r
+import java.awt.*;\r
 \r
 public class SequenceGroup\r
 {\r
   String groupName;\r
-  boolean isSelected;\r
+  Conservation conserve;\r
+  Vector aaFrequency;\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
+  int startRes = 0;\r
+  int endRes = 0;\r
+  Color outlineColour = Color.black;\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 = null;\r
   }\r
 \r
   public SequenceGroup(String groupName, ColourSchemeI scheme,\r
-                       boolean isSelected,\r
                        boolean displayBoxes, boolean displayText,\r
                        boolean colourText,\r
-                       boolean display)\r
+                       int start,\r
+                       int end)\r
   {\r
 \r
     this.groupName = groupName;\r
-    this.isSelected = isSelected;\r
     this.displayBoxes = displayBoxes;\r
     this.displayText = displayText;\r
     this.colourText = colourText;\r
-    this.display = display;\r
     this.cs = scheme;\r
+    startRes = start;\r
+    endRes = end;\r
   }\r
 \r
   public String getName()\r
@@ -75,69 +73,78 @@ public class SequenceGroup
       sequences.addElement(s);\r
   }\r
 \r
+  public void addOrRemove(SequenceI s)\r
+  {\r
+    if(sequences.contains(s))\r
+      deleteSequence(s);\r
+    else\r
+      addSequence(s);\r
+  }\r
+\r
   public void deleteSequence(SequenceI s)\r
   {\r
     sequences.removeElement(s);\r
   }\r
 \r
-  public void setColourText(boolean state)\r
+\r
+  public int getStartRes()\r
   {\r
-    colourText = state;\r
+    return startRes;\r
   }\r
 \r
-  public boolean getColourText()\r
+  public int getEndRes()\r
   {\r
-    return colourText;\r
+    return endRes;\r
   }\r
 \r
-  public void setDisplayText(boolean state)\r
+  public void setStartRes(int i)\r
   {\r
-    displayText = state;\r
+    startRes = i;\r
   }\r
 \r
-  public boolean getDisplayText()\r
+  public void setEndRes(int i)\r
   {\r
-    return displayText;\r
+    endRes = i;\r
   }\r
 \r
-  public void setDisplayBoxes(boolean state)\r
+  public int getSize()\r
   {\r
-    displayBoxes = state;\r
+    return sequences.size();\r
   }\r
 \r
-  public boolean getDisplayBoxes()\r
+  public SequenceI getSequenceAt(int i)\r
   {\r
-    return displayBoxes;\r
+    return (SequenceI) sequences.elementAt(i);\r
   }\r
 \r
-  public int getStartRes()\r
+  public void setColourText(boolean state)\r
   {\r
-    return startRes;\r
+    colourText = state;\r
   }\r
 \r
-  public int getEndRes()\r
+  public boolean getColourText()\r
   {\r
-    return endRes;\r
+    return colourText;\r
   }\r
 \r
-  public void setStartRes(int i)\r
+  public void setDisplayText(boolean state)\r
   {\r
-    startRes = i;\r
+    displayText = state;\r
   }\r
 \r
-  public void setEndRes(int i)\r
+  public boolean getDisplayText()\r
   {\r
-    endRes = i;\r
+    return displayText;\r
   }\r
 \r
-  public int getSize()\r
+  public void setDisplayBoxes(boolean state)\r
   {\r
-    return sequences.size();\r
+    displayBoxes = state;\r
   }\r
 \r
-  public SequenceI getSequenceAt(int i)\r
+  public boolean getDisplayBoxes()\r
   {\r
-    return (SequenceI) sequences.elementAt(i);\r
+    return displayBoxes;\r
   }\r
 \r
   public Vector getAAFrequency()\r
@@ -162,4 +169,14 @@ public class SequenceGroup
     }\r
     return width;\r
   }\r
+\r
+\r
+  public void setOutlineColour(Color c)\r
+  {\r
+    outlineColour = c;\r
+  }\r
+  public Color getOutlineColour()\r
+  {\r
+    return outlineColour;\r
+  }\r
 }\r