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now has a name
author
amwaterhouse
<Andrew Waterhouse>
Tue, 16 Nov 2004 15:14:22 +0000
(15:14 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 16 Nov 2004 15:14:22 +0000
(15:14 +0000)
src/jalview/datamodel/SequenceGroup.java
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diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
de746ba
..
c8b375a
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-1,14
+1,12
@@
package jalview.datamodel;
\r
\r
package jalview.datamodel;
\r
\r
-import jalview.jbgui.*;
\r
import jalview.schemes.*;
\r
import jalview.analysis.*;
\r
import jalview.datamodel.*;
\r
import jalview.schemes.*;
\r
import jalview.analysis.*;
\r
import jalview.datamodel.*;
\r
-
\r
import java.util.Vector;
\r
import java.util.Vector;
\r
-import java.awt.*;
\r
\r
\r
-public class SequenceGroup {
\r
+public class SequenceGroup{
\r
+ String groupName;
\r
boolean isSelected;
\r
boolean displayBoxes;
\r
boolean displayText;
\r
boolean isSelected;
\r
boolean displayBoxes;
\r
boolean displayText;
\r
@@
-17,33
+15,50
@@
public class SequenceGroup {
Conservation conserve;
\r
Vector aaFrequency;
\r
boolean aaFrequencyValid = false;
\r
Conservation conserve;
\r
Vector aaFrequency;
\r
boolean aaFrequencyValid = false;
\r
- Vector sequences = new Vector();
\r
+ public Vector sequences = new Vector();
\r
int width = -1;
\r
int width = -1;
\r
+ public ColourSchemeI cs;
\r
\r
\r
public SequenceGroup() {
\r
\r
\r
public SequenceGroup() {
\r
+ groupName = "Group";
\r
this.isSelected = false;
\r
this.displayBoxes = true;
\r
this.displayText = true;
\r
this.colourText = false;
\r
this.display = true;
\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
}
\r
\r
}
\r
\r
- public SequenceGroup( ColourSchemeI scheme, boolean isSelected,
\r
+ public SequenceGroup( String groupName, ColourSchemeI scheme, boolean isSelected,
\r
boolean displayBoxes, boolean displayText,
\r
boolean colourText,
\r
boolean display) {
\r
\r
boolean displayBoxes, boolean displayText,
\r
boolean colourText,
\r
boolean display) {
\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.isSelected = isSelected;
\r
this.displayBoxes = displayBoxes;
\r
this.displayText = displayText;
\r
this.colourText = colourText;
\r
this.display = display;
\r
+ this.cs = scheme;
\r
+ }
\r
+
\r
+ public String getName()
\r
+ {
\r
+ return groupName;
\r
}
\r
\r
}
\r
\r
+ public void setName(String name)
\r
+ {
\r
+ groupName = name;
\r
+ }
\r
public Conservation getConservation() {
\r
return conserve;
\r
}
\r
public Conservation getConservation() {
\r
return conserve;
\r
}
\r
+ public void setConservation(Conservation c)
\r
+ { conserve = c; }
\r
+
\r
public void addSequence(SequenceI s) {
\r
sequences.addElement(s);
\r
}
\r
public void addSequence(SequenceI s) {
\r
sequences.addElement(s);
\r
}
\r
@@
-84,22
+99,21
@@
public class SequenceGroup {
\r
public Vector getAAFrequency() {
\r
if (aaFrequency == null || aaFrequencyValid == false) {
\r
\r
public Vector getAAFrequency() {
\r
if (aaFrequency == null || aaFrequencyValid == false) {
\r
- aaFrequency = AAFrequency.calculate(sequences,1,getWidth());
\r
+ aaFrequency = AAFrequency.calculate(sequences,0,getWidth());
\r
aaFrequencyValid = true;
\r
}
\r
return aaFrequency;
\r
}
\r
aaFrequencyValid = true;
\r
}
\r
return aaFrequency;
\r
}
\r
- public int getWidth() {
\r
- // MC This needs to get reset when characters are inserted and deleted
\r
- if (width == -1) {
\r
- for (int i = 0; i < sequences.size(); i++) {
\r
- SequenceI seq = (SequenceI)sequences.elementAt(i);
\r
- if (seq.getLength() > width) {
\r
- width = seq.getLength();
\r
- }
\r
- }
\r
- }
\r
\r
\r
+ public int getWidth()
\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
}
\r
}
\r
return width;
\r
}
\r
}
\r