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uses jalviewfilechooser
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
1c6c453
..
2f40de4
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-21,11
+21,14
@@
public class AlignViewport
boolean showBoxes=true;
\r
boolean wrapAlignment=false;
\r
boolean renderGaps = true;
\r
boolean showBoxes=true;
\r
boolean wrapAlignment=false;
\r
boolean renderGaps = true;
\r
+ boolean showSequenceFeatures = false;
\r
\r
\r
+ boolean colourAppliesToAllGroups = true;
\r
ColourSchemeI globalColourScheme = null;
\r
boolean conservationColourSelected = false;
\r
ColourSchemeI globalColourScheme = null;
\r
boolean conservationColourSelected = false;
\r
+ boolean abovePIDThreshold = false;
\r
\r
\r
- SequenceGroup rubberbandGroup = null;
\r
+ SequenceGroup selectionGroup = new SequenceGroup();
\r
\r
RendererI renderer = new SequenceRenderer(this);
\r
\r
\r
RendererI renderer = new SequenceRenderer(this);
\r
\r
@@
-37,11
+40,8
@@
public class AlignViewport
Font font = new Font("SansSerif",Font.PLAIN,10);
\r
AlignmentI alignment;
\r
\r
Font font = new Font("SansSerif",Font.PLAIN,10);
\r
AlignmentI alignment;
\r
\r
- Selection sel = new Selection(this);
\r
ColumnSelection colSel = new ColumnSelection();
\r
\r
ColumnSelection colSel = new ColumnSelection();
\r
\r
- OutputGenerator og;
\r
-
\r
String visibleConsensus;
\r
\r
int threshold;
\r
String visibleConsensus;
\r
\r
int threshold;
\r
@@
-49,10
+49,6
@@
public class AlignViewport
\r
NJTree currentTree = null;
\r
\r
\r
NJTree currentTree = null;
\r
\r
- int window = 50;
\r
- int baseline = 30;
\r
-
\r
- Vector kmers;
\r
\r
public AlignViewport(AlignmentI da,
\r
boolean showScores,
\r
\r
public AlignViewport(AlignmentI da,
\r
boolean showScores,
\r
@@
-89,6
+85,10
@@
public class AlignViewport
setFont( font );
\r
}
\r
\r
setFont( font );
\r
}
\r
\r
+ public void showSequenceFeatures(boolean b)
\r
+ {
\r
+ showSequenceFeatures = b;
\r
+ }
\r
\r
public String getVisibleConsensus()
\r
{
\r
\r
public String getVisibleConsensus()
\r
{
\r
@@
-115,16
+115,17
@@
public class AlignViewport
return consensus;
\r
}
\r
\r
return consensus;
\r
}
\r
\r
- public SequenceGroup getRubberbandGroup()
\r
+ public SequenceGroup getSelectionGroup()
\r
{
\r
{
\r
- return rubberbandGroup;
\r
+ return selectionGroup;
\r
}
\r
\r
}
\r
\r
- public void setRubberbandGroup(SequenceGroup sg)
\r
+ public void setSelectionGroup(SequenceGroup sg)
\r
{
\r
{
\r
- rubberbandGroup = sg;
\r
+ selectionGroup = sg;
\r
}
\r
\r
}
\r
\r
+
\r
public boolean getConservationSelected()
\r
{
\r
return conservationColourSelected;
\r
public boolean getConservationSelected()
\r
{
\r
return conservationColourSelected;
\r
@@
-135,6
+136,16
@@
public class AlignViewport
conservationColourSelected = b;
\r
}
\r
\r
conservationColourSelected = b;
\r
}
\r
\r
+ public boolean getAbovePIDThreshold()
\r
+ {
\r
+ return abovePIDThreshold;
\r
+ }
\r
+
\r
+ public void setAbovePIDThreshold(boolean b)
\r
+ {
\r
+ abovePIDThreshold = b;
\r
+ }
\r
+
\r
public int getStartRes() {
\r
return startRes;
\r
}
\r
public int getStartRes() {
\r
return startRes;
\r
}
\r
@@
-314,15
+325,11
@@
public class AlignViewport
}
\r
return -1;
\r
}
\r
}
\r
return -1;
\r
}
\r
- public Selection getSelection() {
\r
- return sel;
\r
- }
\r
+
\r
public ColumnSelection getColumnSelection() {
\r
return colSel;
\r
}
\r
public ColumnSelection getColumnSelection() {
\r
return colSel;
\r
}
\r
- public OutputGenerator getOutputGenerator() {
\r
- return og;
\r
- }
\r
+
\r
public void resetSeqLimits(int height) {
\r
setStartSeq(0);
\r
setEndSeq(height/getCharHeight());
\r
public void resetSeqLimits(int height) {
\r
setStartSeq(0);
\r
setEndSeq(height/getCharHeight());
\r
@@
-341,27
+348,12
@@
public class AlignViewport
public RendererI getRenderer() {
\r
return renderer;
\r
}
\r
public RendererI getRenderer() {
\r
return renderer;
\r
}
\r
- public int getPIDWindow() {
\r
- return window;
\r
- }
\r
- public void setPIDWindow(int window) {
\r
- this.window = window;
\r
- }
\r
\r
\r
- public int getPIDBaseline() {
\r
- return baseline;
\r
- }
\r
- public void setPIDBaseline(int baseline) {
\r
- this.baseline = baseline;
\r
- }
\r
+ public void setColourAppliesToAllGroups(boolean b)
\r
+ { colourAppliesToAllGroups = b; }
\r
\r
\r
- public void setKmers(Vector kmers) {
\r
- this.kmers = kmers;
\r
- }
\r
-
\r
- public Vector getKmers() {
\r
- return this.kmers;
\r
- }
\r
+ public boolean getColourAppliesToAllGroups()
\r
+ {return colourAppliesToAllGroups; }
\r
\r
\r
}
\r
\r
\r
}
\r