SuperGroups added

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index dd02bc1..f78f958 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -11,7 +11,8 @@ public class Alignment implements AlignmentI
 \r
   protected Vector      sequences;\r
   protected Vector      groups = new Vector();\r
-  protected char      gapCharacter = '-';\r
+  protected ArrayList   superGroup = new ArrayList();\r
+  protected char        gapCharacter = '-';\r
 \r
   /** Make an alignment from an array of Sequences.\r
   *\r
@@ -328,6 +329,7 @@ public class Alignment implements AlignmentI
     for (int i = 0; i < this.groups.size();i++)\r
     {\r
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+\r
       if (sg.sequences.contains(s))\r
        temp.add(sg);\r
     }\r
@@ -356,17 +358,37 @@ public class Alignment implements AlignmentI
     }\r
   }\r
 \r
+  public void addSuperGroup(SuperGroup sg)\r
+  {\r
+    superGroup.add(sg);\r
+  }\r
+\r
+  public void removeSuperGroup(SuperGroup sg)\r
+  {\r
+    superGroup.remove(sg);\r
+  }\r
+\r
+  public SuperGroup     getSuperGroup(SequenceGroup sg)\r
+  {\r
+    for (int i = 0; i < this.superGroup.size(); i++)\r
+    {\r
+      SuperGroup temp = (SuperGroup) superGroup.get(i);\r
+      if (temp.sequenceGroups.contains(sg))\r
+        return temp;\r
+    }\r
+    return null;\r
+  }\r
+\r
   /**    */\r
   public void addGroup(SequenceGroup sg) {\r
     if(!groups.contains(sg))\r
       groups.addElement(sg);\r
   }\r
 \r
-  /**    */\r
-  public SequenceGroup addGroup() {\r
-    SequenceGroup sg = new SequenceGroup();\r
-    groups.addElement(sg);\r
-    return sg;\r
+  public void deleteAllGroups()\r
+  {\r
+    groups.clear();\r
+    superGroup.clear();\r
   }\r
 \r
   /**    */\r

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 660a4fa..80b22ae 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -29,7 +29,7 @@ public interface AlignmentI {
   public void        insertColumns(SequenceI[] seqs, int pos) ;\r
 \r
   public SequenceI   findName(String name) ;\r
-  public SequenceI findbyDisplayId(String name);\r
+  public SequenceI   findbyDisplayId(String name);\r
 \r
   public int         findIndex(SequenceI s) ;\r
 \r
@@ -48,9 +48,13 @@ public interface AlignmentI {
   public void          addToGroup(SequenceGroup g, SequenceI s) ;\r
   public void          removeFromGroup(SequenceGroup g,SequenceI s) ;\r
   public void          addGroup(SequenceGroup sg) ;\r
-  public SequenceGroup addGroup() ;\r
   public void          deleteGroup(SequenceGroup g) ;\r
   public Vector        getGroups();\r
+  public void deleteAllGroups();\r
+\r
+  public void          addSuperGroup(SuperGroup sg);\r
+  public void          removeSuperGroup(SuperGroup sg);\r
+  public SuperGroup    getSuperGroup(SequenceGroup sg);\r
 \r
   // Sorting\r
   public void          sortGroups() ;\r

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index d8c5c93..4d7509d 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -8,13 +8,11 @@ import java.util.Vector;
 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
@@ -25,29 +23,23 @@ public class SequenceGroup
   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
@@ -92,64 +84,65 @@ public class SequenceGroup
     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

diff --git a/src/jalview/datamodel/SuperGroup.java b/src/jalview/datamodel/SuperGroup.java
new file mode 100755 (executable)
index 0000000..6c4da29
--- /dev/null
+++ b/src/jalview/datamodel/SuperGroup.java
@@ -0,0 +1,95 @@
+package jalview.datamodel;\r
+\r
+import jalview.schemes.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
+public class SuperGroup\r
+{\r
+  String groupName;\r
+  boolean displayBoxes;\r
+  boolean displayText;\r
+  boolean colourText;\r
+  public ColourSchemeI cs;\r
+  ArrayList sequenceGroups = new ArrayList();\r
+\r
+  public SuperGroup()\r
+  {\r
+    groupName = "Super group";\r
+    this.displayBoxes = true;\r
+    this.displayText = true;\r
+    this.colourText = false;\r
+    cs = null;\r
+  }\r
+\r
+\r
+  public SuperGroup(String groupName, ColourSchemeI scheme,\r
+                       boolean displayBoxes, boolean displayText,\r
+                       boolean colourText)\r
+     {\r
+       this.groupName = groupName;\r
+       this.displayBoxes = displayBoxes;\r
+       this.displayText = displayText;\r
+       this.colourText = colourText;\r
+       this.cs = scheme;\r
+     }\r
+\r
+  public String getName()\r
+  {\r
+    return groupName;\r
+  }\r
+\r
+  public void setName(String name)\r
+  {\r
+    groupName = name;\r
+  }\r
+\r
+\r
+  public void addGroup(SequenceGroup sg)\r
+  {\r
+    if(!sequenceGroups.contains(sg))\r
+      sequenceGroups.add(sg);\r
+  }\r
+\r
+  public void addOrRemove(SequenceGroup sg)\r
+  {\r
+    if(sequenceGroups.contains(sg))\r
+      deleteGroup(sg);\r
+    else\r
+      addGroup(sg);\r
+  }\r
+\r
+  public void deleteGroup(SequenceGroup sg)\r
+  {\r
+    sequenceGroups.remove(sg);\r
+  }\r
+\r
+  public void setSuperGroupProperties(SequenceGroup sg)\r
+  {\r
+    cs = sg.cs;\r
+    colourText = sg.colourText;\r
+    displayText = sg.displayText;\r
+    displayBoxes = sg.displayBoxes;\r
+\r
+    for(int i=0; i<sequenceGroups.size(); i++)\r
+    {\r
+      SequenceGroup temp = (SequenceGroup)sequenceGroups.get(i);\r
+      temp.cs = sg.cs;\r
+      temp.colourText = sg.colourText;\r
+      temp.displayText = sg.displayText;\r
+      temp.displayBoxes = sg.displayBoxes;\r
+    }\r
+  }\r
+\r
+\r
+  public int getSize()\r
+  {\r
+    return sequenceGroups.size();\r
+  }\r
+\r
+  public SequenceGroup getGroupeAt(int i)\r
+  {\r
+    return (SequenceGroup) sequenceGroups.get(i);\r
+  }\r
+}\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 500bf84..1d6cbf4 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -202,6 +202,13 @@ public class AlignFrame extends GAlignFrame
     frame.setResizable(false);\r
   }\r
 \r
+  protected void deleteGroups_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.alignment.deleteAllGroups();\r
+    alignPanel.RefreshPanels();\r
+  }\r
+\r
+\r
 \r
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -312,8 +319,9 @@ public class AlignFrame extends GAlignFrame
     JOptionPane op = new JOptionPane();\r
     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
     Finder finder = new Finder(viewport, alignPanel, frame);\r
+    frame.setClosable(true);\r
     frame.setContentPane(finder);\r
-    frame.setSize(300,110);\r
+    frame.setSize(340,110);\r
     frame.setVisible(true);\r
   }\r
 \r
@@ -518,6 +526,13 @@ public class AlignFrame extends GAlignFrame
     changeColour();\r
   }\r
 \r
+  public void nucleotideColour_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
+    changeColour();\r
+  }\r
+\r
+\r
   void changeColour()\r
   {\r
     if(abovePIDThreshold.isSelected())\r