/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import java.util.*;\r
+\r
import java.awt.*;\r
+\r
import jalview.analysis.*;\r
-import jalview.analysis.NJTree;\r
+import jalview.bin.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.util.*;\r
-import jalview.bin.Cache;\r
\r
public class AlignViewport\r
{\r
int startRes;\r
int endRes;\r
-\r
int startSeq;\r
int endSeq;\r
-\r
boolean showFullId = false;\r
- boolean showText=true;\r
- boolean showColourText=false;\r
- boolean showBoxes=true;\r
- boolean wrapAlignment=false;\r
+ boolean showText = true;\r
+ boolean showColourText = false;\r
+ boolean showBoxes = true;\r
+ boolean wrapAlignment = false;\r
boolean renderGaps = true;\r
boolean showSequenceFeatures = false;\r
boolean showAnnotation = true;\r
boolean showConservation = true;\r
boolean showQuality = true;\r
boolean showIdentity = true;\r
-\r
boolean colourAppliesToAllGroups = true;\r
ColourSchemeI globalColourScheme = null;\r
boolean conservationColourSelected = false;\r
boolean abovePIDThreshold = false;\r
-\r
SequenceGroup selectionGroup = new SequenceGroup();\r
-\r
-\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
-\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
-\r
+ int charHeight;\r
+ int charWidth;\r
+ int chunkWidth;\r
+ int chunkHeight;\r
+ Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ AlignmentI alignment;\r
ColumnSelection colSel = new ColumnSelection();\r
-\r
int threshold;\r
int increment;\r
-\r
NJTree currentTree = null;\r
-\r
boolean scaleAboveWrapped = false;\r
- boolean scaleLeftWrapped = true;\r
+ boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
+ public Vector vconsensus;\r
+ AlignmentAnnotation consensus;\r
+ AlignmentAnnotation conservation;\r
+ AlignmentAnnotation quality;\r
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
+ // JBPNote Prolly only need this in the applet version.\r
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.\r
+ PropertyChangeSupport(this);\r
\r
public AlignViewport(AlignmentI al)\r
{\r
setAlignment(al);\r
this.startRes = 0;\r
- this.endRes = al.getWidth()-1;\r
+ this.endRes = al.getWidth() - 1;\r
this.startSeq = 0;\r
- this.endSeq = al.getHeight()-1;\r
+ this.endSeq = al.getHeight() - 1;\r
\r
updateFromPreferences();\r
-\r
}\r
\r
public void updateFromPreferences()\r
showQuality = Preferences.showQuality;\r
showIdentity = Preferences.showIdentity;\r
showFullId = Preferences.showFullId;\r
+\r
String fontName = Preferences.fontName;\r
String fontStyle = Preferences.fontStyle;\r
String fontSize = Cache.getProperty("FONT_SIZE");\r
- if (fontName != null && fontStyle != null && fontSize != null)\r
+\r
+ if ( (fontName != null) && (fontStyle != null) && (fontSize != null))\r
{\r
int style = 0;\r
- if(fontStyle.equals("bold"))\r
+\r
+ if (fontStyle.equals("bold"))\r
+ {\r
style = 1;\r
- else if(fontStyle.equals("italic"))\r
+ }\r
+ else if (fontStyle.equals("italic"))\r
+ {\r
style = 2;\r
+ }\r
+\r
setFont(new Font(fontName, style, Integer.parseInt(fontSize)));\r
}\r
else\r
+ {\r
setFont(font);\r
+ }\r
\r
alignment.setGapCharacter(Preferences.gapSymbol);\r
\r
// as Blosum and Clustal require this to be done\r
updateConservation();\r
updateConsensus();\r
- if(Preferences.defaultColour!=null)\r
+\r
+ if (Preferences.defaultColour != null)\r
{\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);\r
- if(globalColourScheme instanceof UserColourScheme)\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
+ Preferences.defaultColour);\r
+\r
+ if (globalColourScheme instanceof UserColourScheme)\r
{\r
globalColourScheme = UserDefinedColours.loadDefaultColours();\r
}\r
- if(globalColourScheme!=null)\r
- globalColourScheme.setConsensus( vconsensus );\r
- }\r
-\r
- }\r
\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- public Vector vconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+ }\r
+ }\r
\r
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+ public void showSequenceFeatures(boolean b)\r
+ {\r
+ showSequenceFeatures = b;\r
+ }\r
\r
public void updateConservation()\r
{\r
Conservation cons = new jalview.analysis.Conservation("All",\r
jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0,\r
- alignment.getWidth()-1);\r
+ alignment.getSequences(), 0, alignment.getWidth() - 1);\r
cons.calculate();\r
cons.verdict(false, ConsPercGaps);\r
cons.findQuality();\r
+\r
int alWidth = alignment.getWidth();\r
- Annotation [] annotations = new Annotation[alWidth];\r
- Annotation [] qannotations = new Annotation[alWidth];\r
+ Annotation[] annotations = new Annotation[alWidth];\r
+ Annotation[] qannotations = new Annotation[alWidth];\r
String sequence = cons.getConsSequence().getSequence();\r
- float minR,minG,minB, maxR,maxG,maxB;\r
+ float minR;\r
+ float minG;\r
+ float minB;\r
+ float maxR;\r
+ float maxG;\r
+ float maxB;\r
minR = 0.3f;\r
minG = 0.0f;\r
minB = 0f;\r
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality\r
+ maxR = 1.0f - minR;\r
+ maxG = 0.9f - minG;\r
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
+\r
float min = 0f;\r
float max = 11f;\r
float qmin = cons.qualityRange[0].floatValue();\r
for (int i = 0; i < alWidth; i++)\r
{\r
float value = 0;\r
+\r
try\r
+ {\r
+ value = Integer.parseInt(sequence.charAt(i) + "");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ if (sequence.charAt(i) == '*')\r
{\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
+ value = 11;\r
}\r
- catch (Exception ex)\r
+\r
+ if (sequence.charAt(i) == '+')\r
{\r
- if (sequence.charAt(i) == '*') value = 11;\r
- if (sequence.charAt(i) == '+') value = 10;\r
+ value = 10;\r
}\r
- float vprop = value-min;\r
- vprop/=max;\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ }\r
+\r
+ float vprop = value - min;\r
+ vprop /= max;\r
+ annotations[i] = new Annotation(sequence.charAt(i) + "", "", ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+\r
// Quality calc\r
- value = ((Double) cons.quality.get(i)).floatValue();\r
+ value = ( (Double) cons.quality.get(i)).floatValue();\r
vprop = value - qmin;\r
- vprop/=qmax;\r
- qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ vprop /= qmax;\r
+ qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
}\r
\r
- if(conservation==null)\r
+ if (conservation == null)\r
{\r
conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than "+ConsPercGaps+"% gaps",\r
- annotations,\r
- 0f, // cons.qualityRange[0].floatValue(),\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
+ annotations, 0f, // cons.qualityRange[0].floatValue(),\r
11f, // cons.qualityRange[1].floatValue()\r
1);\r
- if(showConservation)\r
- alignment.addAnnotation(conservation);\r
+\r
+ if (showConservation)\r
+ {\r
+ alignment.addAnnotation(conservation);\r
+ }\r
+\r
quality = new AlignmentAnnotation("Quality",\r
"Alignment Quality based on Blosum62 scores",\r
qannotations,\r
cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(),\r
- 1);\r
- if(showQuality)\r
+ cons.qualityRange[1].floatValue(), 1);\r
+\r
+ if (showQuality)\r
+ {\r
alignment.addAnnotation(quality);\r
+ }\r
}\r
- else {\r
+ else\r
+ {\r
conservation.annotations = annotations;\r
quality.annotations = qannotations;\r
quality.graphMax = cons.qualityRange[1].floatValue();\r
}\r
-\r
-\r
}\r
\r
public void updateConsensus()\r
{\r
- Annotation [] annotations = new Annotation[alignment.getWidth()];\r
+ Annotation[] annotations = new Annotation[alignment.getWidth()];\r
\r
// this routine prevents vconsensus becoming a new object each time\r
// consenus is calculated. Important for speed of Blosum62\r
// and PID colouring of alignment\r
- if(vconsensus == null)\r
- vconsensus = alignment.getAAFrequency();\r
+ if (vconsensus == null)\r
+ {\r
+ vconsensus = alignment.getAAFrequency();\r
+ }\r
else\r
{\r
- Vector temp = alignment.getAAFrequency();\r
- vconsensus.clear();\r
- Enumeration e = temp.elements();\r
- while(e.hasMoreElements())\r
- {\r
- vconsensus.add(e.nextElement());\r
- }\r
+ Vector temp = alignment.getAAFrequency();\r
+ vconsensus.clear();\r
+\r
+ Enumeration e = temp.elements();\r
+\r
+ while (e.hasMoreElements())\r
+ {\r
+ vconsensus.add(e.nextElement());\r
+ }\r
}\r
+\r
Hashtable hash = null;\r
- for (int i = 0; i<alignment.getWidth(); i++)\r
+\r
+ for (int i = 0; i < alignment.getWidth(); i++)\r
{\r
- hash = (Hashtable) vconsensus.elementAt(i);\r
- float value = Float.parseFloat(hash.get("maxCount").toString());\r
- value /= Float.parseFloat(hash.get("size").toString());\r
-\r
- value *= 100;\r
- String maxRes = hash.get("maxResidue")+" ";\r
- String mouseOver = hash.get("maxResidue")+" ";\r
- if(maxRes.length()>2)\r
- {\r
- mouseOver = "["+maxRes+"] ";\r
- maxRes = "+ ";\r
- }\r
+ hash = (Hashtable) vconsensus.elementAt(i);\r
+\r
+ float value = Float.parseFloat(hash.get("maxCount").toString());\r
+ value /= Float.parseFloat(hash.get("size").toString());\r
+\r
+ value *= 100;\r
\r
- mouseOver += (int)value+"%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ String maxRes = hash.get("maxResidue") + " ";\r
+ String mouseOver = hash.get("maxResidue") + " ";\r
+\r
+ if (maxRes.length() > 2)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+ ";\r
+ }\r
\r
+ mouseOver += ( (int) value + "%");\r
+ annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
}\r
\r
- if(consensus==null)\r
- {\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, 1);\r
- if(showIdentity)\r
- alignment.addAnnotation(consensus);\r
- }\r
- else\r
- consensus.annotations = annotations;\r
+ if (consensus == null)\r
+ {\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ annotations, 0f, 100f, 1);\r
\r
+ if (showIdentity)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ consensus.annotations = annotations;\r
+ }\r
}\r
\r
-\r
public SequenceGroup getSelectionGroup()\r
{\r
return selectionGroup;\r
selectionGroup = sg;\r
}\r
\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+ return abovePIDThreshold;\r
+ }\r
\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+ abovePIDThreshold = b;\r
+ }\r
\r
- public int getStartRes() {\r
+ public int getStartRes()\r
+ {\r
return startRes;\r
}\r
\r
- public int getEndRes() {\r
+ public int getEndRes()\r
+ {\r
return endRes;\r
}\r
\r
- public int getStartSeq() {\r
+ public int getStartSeq()\r
+ {\r
return startSeq;\r
}\r
\r
public void setGlobalColourScheme(ColourSchemeI cs)\r
{\r
- globalColourScheme = cs;\r
+ globalColourScheme = cs;\r
}\r
\r
public ColourSchemeI getGlobalColourScheme()\r
return globalColourScheme;\r
}\r
\r
-\r
- public void setStartRes(int res) {\r
+ public void setStartRes(int res)\r
+ {\r
this.startRes = res;\r
}\r
- public void setStartSeq(int seq) {\r
+\r
+ public void setStartSeq(int seq)\r
+ {\r
this.startSeq = seq;\r
}\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\r
+\r
+ public void setEndRes(int res)\r
+ {\r
+ if (res > (alignment.getWidth() - 1))\r
+ {\r
// log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth()-1;\r
+ res = alignment.getWidth() - 1;\r
}\r
- if (res < 0) {\r
+\r
+ if (res < 0)\r
+ {\r
res = 0;\r
}\r
+\r
this.endRes = res;\r
}\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
+\r
+ public void setEndSeq(int seq)\r
+ {\r
+ if (seq > alignment.getHeight())\r
+ {\r
seq = alignment.getHeight();\r
}\r
- if (seq < 0) {\r
+\r
+ if (seq < 0)\r
+ {\r
seq = 0;\r
}\r
+\r
this.endSeq = seq;\r
}\r
- public int getEndSeq() {\r
+\r
+ public int getEndSeq()\r
+ {\r
return endSeq;\r
}\r
\r
- public void setFont(Font f) {\r
+ public void setFont(Font f)\r
+ {\r
font = f;\r
+\r
javax.swing.JFrame temp = new javax.swing.JFrame();\r
temp.addNotify();\r
+\r
java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\r
setCharHeight(fm.getHeight());\r
setCharWidth(fm.charWidth('M'));\r
}\r
\r
- public Font getFont() {\r
+ public Font getFont()\r
+ {\r
return font;\r
}\r
- public void setCharWidth(int w) {\r
+\r
+ public void setCharWidth(int w)\r
+ {\r
this.charWidth = w;\r
}\r
- public int getCharWidth() {\r
+\r
+ public int getCharWidth()\r
+ {\r
return charWidth;\r
}\r
- public void setCharHeight(int h) {\r
+\r
+ public void setCharHeight(int h)\r
+ {\r
this.charHeight = h;\r
}\r
- public int getCharHeight() {\r
+\r
+ public int getCharHeight()\r
+ {\r
return charHeight;\r
}\r
- public void setChunkWidth(int w) {\r
+\r
+ public void setChunkWidth(int w)\r
+ {\r
this.chunkWidth = w;\r
}\r
- public int getChunkWidth() {\r
+\r
+ public int getChunkWidth()\r
+ {\r
return chunkWidth;\r
}\r
- public void setChunkHeight(int h) {\r
+\r
+ public void setChunkHeight(int h)\r
+ {\r
this.chunkHeight = h;\r
}\r
- public int getChunkHeight() {\r
+\r
+ public int getChunkHeight()\r
+ {\r
return chunkHeight;\r
}\r
- public AlignmentI getAlignment() {\r
+\r
+ public AlignmentI getAlignment()\r
+ {\r
return alignment;\r
}\r
- public void setAlignment(AlignmentI align) {\r
+\r
+ public void setAlignment(AlignmentI align)\r
+ {\r
this.alignment = align;\r
}\r
\r
- public void setWrapAlignment(boolean state) {\r
+ public void setWrapAlignment(boolean state)\r
+ {\r
wrapAlignment = state;\r
}\r
- public void setShowText(boolean state) {\r
+\r
+ public void setShowText(boolean state)\r
+ {\r
showText = state;\r
}\r
\r
- public void setRenderGaps(boolean state){\r
+ public void setRenderGaps(boolean state)\r
+ {\r
renderGaps = state;\r
}\r
\r
-\r
public boolean getColourText()\r
{\r
return showColourText;\r
showColourText = state;\r
}\r
\r
- public void setShowBoxes(boolean state) {\r
+ public void setShowBoxes(boolean state)\r
+ {\r
showBoxes = state;\r
}\r
\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return wrapAlignment;\r
}\r
- public boolean getShowText() {\r
+\r
+ public boolean getShowText()\r
+ {\r
return showText;\r
}\r
- public boolean getShowBoxes() {\r
+\r
+ public boolean getShowBoxes()\r
+ {\r
return showBoxes;\r
}\r
\r
- public char getGapCharacter() {\r
+ public char getGapCharacter()\r
+ {\r
return getAlignment().getGapCharacter();\r
}\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
+\r
+ public void setGapCharacter(char gap)\r
+ {\r
+ if (getAlignment() != null)\r
+ {\r
getAlignment().setGapCharacter(gap);\r
}\r
}\r
- public void setThreshold(int thresh) {\r
+\r
+ public void setThreshold(int thresh)\r
+ {\r
threshold = thresh;\r
}\r
- public int getThreshold() {\r
+\r
+ public int getThreshold()\r
+ {\r
return threshold;\r
}\r
- public void setIncrement(int inc) {\r
+\r
+ public void setIncrement(int inc)\r
+ {\r
increment = inc;\r
}\r
- public int getIncrement() {\r
+\r
+ public int getIncrement()\r
+ {\r
return increment;\r
}\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
+\r
+ public int getIndex(int y)\r
+ {\r
+ int y1 = 0;\r
int starty = getStartSeq();\r
- int endy = getEndSeq();\r
+ int endy = getEndSeq();\r
\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\r
+ for (int i = starty; i <= endy; i++)\r
+ {\r
+ if ( (i < alignment.getHeight()) &&\r
+ (alignment.getSequenceAt(i) != null))\r
+ {\r
int y2 = y1 + getCharHeight();\r
\r
- if (y>=y1 && y <=y2) {\r
+ if ( (y >= y1) && (y <= y2))\r
+ {\r
return i;\r
}\r
- y1 = y2;\r
- } else {\r
+\r
+ y1 = y2;\r
+ }\r
+ else\r
+ {\r
return -1;\r
}\r
}\r
+\r
return -1;\r
}\r
\r
- public ColumnSelection getColumnSelection() {\r
+ public ColumnSelection getColumnSelection()\r
+ {\r
return colSel;\r
}\r
\r
- public void resetSeqLimits(int height) {\r
- setEndSeq(height/getCharHeight());\r
+ public void resetSeqLimits(int height)\r
+ {\r
+ setEndSeq(height / getCharHeight());\r
}\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
+\r
+ public void setCurrentTree(NJTree tree)\r
+ {\r
+ currentTree = tree;\r
}\r
- public NJTree getCurrentTree() {\r
+\r
+ public NJTree getCurrentTree()\r
+ {\r
return currentTree;\r
}\r
\r
public void setColourAppliesToAllGroups(boolean b)\r
- { colourAppliesToAllGroups = b; }\r
+ {\r
+ colourAppliesToAllGroups = b;\r
+ }\r
\r
public boolean getColourAppliesToAllGroups()\r
- {return colourAppliesToAllGroups; }\r
+ {\r
+ return colourAppliesToAllGroups;\r
+ }\r
\r
public boolean getShowFullId()\r
{\r
}\r
\r
public boolean getShowAnnotation()\r
- { return showAnnotation; }\r
+ {\r
+ return showAnnotation;\r
+ }\r
\r
public void setShowAnnotation(boolean b)\r
- { showAnnotation = b; }\r
+ {\r
+ showAnnotation = b;\r
+ }\r
\r
public boolean getScaleAboveWrapped()\r
- { return scaleAboveWrapped;}\r
+ {\r
+ return scaleAboveWrapped;\r
+ }\r
\r
public boolean getScaleLeftWrapped()\r
- { return scaleLeftWrapped; }\r
+ {\r
+ return scaleLeftWrapped;\r
+ }\r
\r
public boolean getScaleRightWrapped()\r
- { return scaleRightWrapped; }\r
+ {\r
+ return scaleRightWrapped;\r
+ }\r
\r
public void setScaleAboveWrapped(boolean b)\r
- { scaleAboveWrapped = b; }\r
+ {\r
+ scaleAboveWrapped = b;\r
+ }\r
\r
public void setScaleLeftWrapped(boolean b)\r
- { scaleLeftWrapped = b; }\r
+ {\r
+ scaleLeftWrapped = b;\r
+ }\r
\r
public void setScaleRightWrapped(boolean b)\r
- { scaleRightWrapped = b; }\r
- // JBPNote Prolly only need this in the applet version.\r
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\r
- public void addPropertyChangeListener(java.beans.PropertyChangeListener listener) {\r
+ {\r
+ scaleRightWrapped = b;\r
+ }\r
+\r
+ public void addPropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
changeSupport.addPropertyChangeListener(listener);\r
}\r
\r
- public void removePropertyChangeListener(java.beans.PropertyChangeListener listener) {\r
+ public void removePropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
changeSupport.removePropertyChangeListener(listener);\r
}\r
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue) {\r
+\r
+ public void firePropertyChange(String prop, Object oldvalue, Object newvalue)\r
+ {\r
changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff