X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=0cf954b44d127b98edebac6c0dc5a6ad342e0972;hb=c1fad33365988bdf8e335982df0c3ff84dd0bb8b;hp=de746ba38a999c133c28352bb86a7635a85335bf;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index de746ba..0cf954b 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,107 +1,219 @@
 package jalview.datamodel;
 
-import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
-
 import java.util.Vector;
 import java.awt.*;
 
-public class SequenceGroup {
-    boolean isSelected;
-    boolean displayBoxes;
-    boolean displayText;
-    boolean colourText;
-    boolean display;
-    Conservation conserve;
-    Vector   aaFrequency;
-    boolean     aaFrequencyValid = false;
-    Vector sequences = new Vector();
-    int         width = -1;
-
-
-  public SequenceGroup() {
-    this.isSelected = false;
+public class SequenceGroup
+{
+  String groupName;
+  Conservation conserve;
+  Vector aaFrequency;
+  boolean displayBoxes;
+  boolean displayText;
+  boolean colourText;
+  boolean aaFrequencyValid = false;
+  public Vector sequences = new Vector();
+  int width = -1;
+  public ColourSchemeI cs;
+  int startRes = 0;
+  int endRes = 0;
+  Color outlineColour = Color.black;
+
+  public SequenceGroup()
+  {
+    groupName = "Group";
     this.displayBoxes = true;
     this.displayText = true;
     this.colourText = false;
-    this.display = true;
+    cs = null;
   }
 
-  public SequenceGroup( ColourSchemeI scheme, boolean isSelected,
-                        boolean displayBoxes, boolean displayText,
-                        boolean colourText,
-                        boolean display) {
+  public SequenceGroup(String groupName, ColourSchemeI scheme,
+                       boolean displayBoxes, boolean displayText,
+                       boolean colourText,
+                       int start,
+                       int end)
+  {
 
-    this.isSelected = isSelected;
+    this.groupName = groupName;
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
-    this.display = display;
+    this.cs = scheme;
+    startRes = start;
+    endRes = end;
+  }
+
+  public boolean adjustForRemoveLeft(int col)
+  {
+    // return value is true if the group still exists
+    if(startRes>=col)
+      startRes = startRes - col;
+    if(endRes>=col)
+    {
+      endRes = endRes - col;
+      if(startRes>endRes)
+        startRes = 0;
+    }
+    else
+    {
+        // must delete this group!!
+        return false;
+    }
+
+    return true;
   }
 
-  public Conservation getConservation() {
-     return conserve;
+  public boolean adjustForRemoveRight(int col)
+  {
+
+    if(startRes>col)
+    {
+      // delete this group
+      return false;
+    }
+
+    if(endRes>=col)
+      endRes = col;
+
+
+    return true;
   }
-  public void addSequence(SequenceI s) {
-    sequences.addElement(s);
+
+
+  public String getName()
+  {
+    return groupName;
+  }
+
+  public void setName(String name)
+  {
+    groupName = name;
+  }
+
+  public Conservation getConservation()
+  {
+    return conserve;
+  }
+
+  public void setConservation(Conservation c)
+  {
+    conserve = c;
+  }
+
+  public void addSequence(SequenceI s)
+  {
+    if(!sequences.contains(s))
+      sequences.addElement(s);
+  }
+
+  public void addOrRemove(SequenceI s)
+  {
+    if(sequences.contains(s))
+      deleteSequence(s);
+    else
+      addSequence(s);
   }
 
-  public void deleteSequence(SequenceI s) {
+  public void deleteSequence(SequenceI s)
+  {
     sequences.removeElement(s);
   }
 
-  public void setColourText(boolean state) {
+
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  public void setStartRes(int i)
+  {
+    startRes = i;
+  }
+
+  public void setEndRes(int i)
+  {
+    endRes = i;
+  }
+
+  public int getSize()
+  {
+    return sequences.size();
+  }
+
+  public SequenceI getSequenceAt(int i)
+  {
+    return (SequenceI) sequences.elementAt(i);
+  }
+
+  public void setColourText(boolean state)
+  {
     colourText = state;
   }
-  public boolean getColourText() {
+
+  public boolean getColourText()
+  {
     return colourText;
   }
 
-  public void setDisplayText(boolean state) {
+  public void setDisplayText(boolean state)
+  {
     displayText = state;
   }
 
-  public boolean getDisplayText() {
+  public boolean getDisplayText()
+  {
     return displayText;
   }
 
-  public void setDisplayBoxes(boolean state) {
+  public void setDisplayBoxes(boolean state)
+  {
     displayBoxes = state;
   }
 
-  public boolean getDisplayBoxes() {
+  public boolean getDisplayBoxes()
+  {
     return displayBoxes;
   }
 
-    public int getSize() {
-	return sequences.size();
-    }
-    public SequenceI  getSequenceAt(int i) {
-	return (SequenceI)sequences.elementAt(i);
+  public Vector getAAFrequency()
+  {
+    if (aaFrequency == null || aaFrequencyValid == false)
+    {
+      aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
+      aaFrequencyValid = true;
     }
+    return aaFrequency;
+  }
 
-    public Vector getAAFrequency() {
-	if (aaFrequency == null || aaFrequencyValid == false) {
-	    aaFrequency = AAFrequency.calculate(sequences,1,getWidth());
-	    aaFrequencyValid = true;
-	}
-	return aaFrequency;
-    }
-    public int getWidth() {
-	// MC This needs to get reset when characters are inserted and deleted
-	if (width == -1) {
-	    for (int i = 0; i < sequences.size(); i++) {
-		SequenceI seq = (SequenceI)sequences.elementAt(i);
-		if (seq.getLength() > width) {
-		    width = seq.getLength();
-		}
-	    }
-	}
-
-	return width;
+  public int getWidth()
+  {
+    System.out.println("it is called");
+    // MC This needs to get reset when characters are inserted and deleted
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      SequenceI seq = (SequenceI) sequences.elementAt(i);
+      if (seq.getLength() > width)
+        width = seq.getLength();
     }
-}
+    return width;
+  }
 
 
+  public void setOutlineColour(Color c)
+  {
+    outlineColour = c;
+  }
+  public Color getOutlineColour()
+  {
+    return outlineColour;
+  }
+}