/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
int startSeq;\r
int endSeq;\r
\r
-\r
boolean cursorMode = false;\r
\r
boolean showJVSuffix = true;\r
boolean scaleRightWrapped = true;\r
\r
// The following vector holds the features which are\r
- // currently visible, in the correct order or rendering\r
+ // currently visible, in the correct order or rendering\r
public Hashtable featuresDisplayed;\r
\r
boolean hasHiddenColumns = false;\r
boolean hasHiddenRows = false;\r
boolean showHiddenMarkers = true;\r
\r
-\r
- public Hashtable [] hconsensus;\r
+ public Hashtable[] hconsensus;\r
AlignmentAnnotation consensus;\r
AlignmentAnnotation conservation;\r
AlignmentAnnotation quality;\r
\r
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\r
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.\r
+ PropertyChangeSupport(this);\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
this.endSeq = al.getHeight() - 1;\r
setFont(font);\r
\r
- if(System.getProperty("os.name").startsWith("Mac"))\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
MAC = true;\r
+ }\r
\r
if (applet != null)\r
{\r
param = applet.getParameter("upperCase");\r
if (param != null)\r
{\r
- if(param.equalsIgnoreCase("bold"))\r
+ if (param.equalsIgnoreCase("bold"))\r
+ {\r
upperCasebold = true;\r
+ }\r
}\r
\r
}\r
{\r
String colour = applet.getParameter("defaultColour");\r
\r
- if(colour == null)\r
+ if (colour == null)\r
{\r
colour = applet.getParameter("userDefinedColour");\r
- if(colour !=null)\r
+ if (colour != null)\r
+ {\r
colour = "User Defined";\r
+ }\r
}\r
\r
- if(colour != null)\r
+ if (colour != null)\r
{\r
globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
if (globalColourScheme != null)\r
}\r
}\r
\r
- if(applet.getParameter("userDefinedColour")!=null)\r
+ if (applet.getParameter("userDefinedColour") != null)\r
{\r
- ((UserColourScheme)globalColourScheme).parseAppletParameter(\r
+ ( (UserColourScheme) globalColourScheme).parseAppletParameter(\r
applet.getParameter("userDefinedColour"));\r
}\r
\r
- if(hconsensus==null)\r
+ if (hconsensus == null)\r
{\r
- if(!alignment.isNucleotide())\r
+ if (!alignment.isNucleotide())\r
{\r
conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than " +\r
- ConsPercGaps + "% gaps",\r
- new Annotation[1], 0f,\r
- 11f,\r
- AlignmentAnnotation.BAR_GRAPH);\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
+ new Annotation[1], 0f,\r
+ 11f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
conservation.hasText = true;\r
conservation.autoCalculated = true;\r
\r
-\r
-\r
if (showConservation)\r
{\r
alignment.addAnnotation(conservation);\r
}\r
\r
consensus = new AlignmentAnnotation("Consensus", "PID",\r
- new Annotation[1], 0f, 100f,\r
- AlignmentAnnotation.BAR_GRAPH);\r
+ new Annotation[1], 0f, 100f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
consensus.hasText = true;\r
consensus.autoCalculated = true;\r
\r
- if (showConsensus)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
+ if (showConsensus)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
}\r
}\r
}\r
return showSequenceFeatures;\r
}\r
\r
-\r
- class ConservationThread extends Thread\r
+ class ConservationThread\r
+ extends Thread\r
{\r
AlignmentPanel ap;\r
public ConservationThread(AlignmentPanel ap)\r
\r
UPDATING_CONSERVATION = true;\r
\r
-\r
int alWidth = alignment.getWidth();\r
- if(alWidth<0)\r
+ if (alWidth < 0)\r
+ {\r
return;\r
+ }\r
\r
Conservation cons = new jalview.analysis.Conservation("All",\r
jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0, alWidth -1);\r
+ alignment.getSequences(), 0, alWidth - 1);\r
\r
cons.calculate();\r
cons.verdict(false, ConsPercGaps);\r
\r
- if (quality!=null)\r
+ if (quality != null)\r
{\r
cons.findQuality();\r
}\r
\r
- char [] sequence = cons.getConsSequence().getSequence();\r
+ char[] sequence = cons.getConsSequence().getSequence();\r
float minR;\r
float minG;\r
float minB;\r
\r
conservation.annotations = new Annotation[alWidth];\r
\r
- if (quality!=null)\r
+ if (quality != null)\r
{\r
quality.graphMax = cons.qualityRange[1].floatValue();\r
quality.annotations = new Annotation[alWidth];\r
c = sequence[i];\r
\r
if (Character.isDigit(c))\r
+ {\r
value = (int) (c - '0');\r
+ }\r
else if (c == '*')\r
+ {\r
value = 11;\r
+ }\r
else if (c == '+')\r
+ {\r
value = 10;\r
+ }\r
\r
float vprop = value - min;\r
vprop /= max;\r
minB + (maxB * vprop)));\r
\r
// Quality calc\r
- if (quality!=null)\r
+ if (quality != null)\r
{\r
value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
vprop = value - qmin;\r
vprop /= qmax;\r
- quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
- value,\r
- new Color(minR + (maxR * vprop),\r
- minG + (maxG * vprop),\r
- minB + (maxB * vprop)));\r
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value),\r
+ ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
}\r
}\r
}\r
UPDATING_CONSERVATION = false;\r
updatingConservation = false;\r
\r
- if(ap!=null)\r
+ if (ap != null)\r
{\r
ap.repaint();\r
}\r
}\r
}\r
\r
-\r
ConservationThread conservationThread;\r
\r
ConsensusThread consensusThread;\r
*/\r
public void updateConservation(final AlignmentPanel ap)\r
{\r
- if (alignment.isNucleotide() || conservation==null)\r
+ if (alignment.isNucleotide() || conservation == null)\r
+ {\r
return;\r
+ }\r
\r
conservationThread = new ConservationThread(ap);\r
conservationThread.start();\r
consensusThread.start();\r
}\r
\r
-\r
- class ConsensusThread extends Thread\r
+ class ConsensusThread\r
+ extends Thread\r
{\r
AlignmentPanel ap;\r
public ConsensusThread(AlignmentPanel ap)\r
{\r
this.ap = ap;\r
}\r
+\r
public void run()\r
{\r
updatingConsensus = true;\r
}\r
}\r
\r
-\r
UPDATING_CONSENSUS = true;\r
\r
try\r
{\r
int aWidth = alignment.getWidth();\r
- if(aWidth<0)\r
+ if (aWidth < 0)\r
+ {\r
return;\r
+ }\r
\r
consensus.annotations = null;\r
consensus.annotations = new Annotation[aWidth];\r
\r
-\r
hconsensus = new Hashtable[aWidth];\r
AAFrequency.calculate(alignment.getSequencesArray(),\r
0,\r
{\r
float value = 0;\r
if (ignoreGapsInConsensusCalculation)\r
+ {\r
value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).\r
floatValue();\r
+ }\r
else\r
+ {\r
value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).\r
floatValue();\r
+ }\r
\r
String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";\r
}\r
\r
mouseOver += ( (int) value + "%");\r
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',\r
+ value);\r
}\r
\r
-\r
if (globalColourScheme != null)\r
+ {\r
globalColourScheme.setConsensus(hconsensus);\r
+ }\r
\r
}\r
catch (OutOfMemoryError error)\r
*/\r
public SequenceI getConsensusSeq()\r
{\r
- if (consensus==null)\r
+ if (consensus == null)\r
+ {\r
return null;\r
- StringBuffer seqs=new StringBuffer();\r
- for (int i=0; i<consensus.annotations.length; i++) {\r
- if (consensus.annotations[i]!=null) {\r
+ }\r
+ StringBuffer seqs = new StringBuffer();\r
+ for (int i = 0; i < consensus.annotations.length; i++)\r
+ {\r
+ if (consensus.annotations[i] != null)\r
+ {\r
if (consensus.annotations[i].description.charAt(0) == '[')\r
+ {\r
seqs.append(consensus.annotations[i].description.charAt(1));\r
+ }\r
else\r
+ {\r
seqs.append(consensus.annotations[i].displayCharacter);\r
+ }\r
}\r
}\r
SequenceI sq = new Sequence("Consensus", seqs.toString());\r
- sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));\r
+ sq.setDescription("Percentage Identity Consensus " +\r
+ ( (ignoreGapsInConsensusCalculation) ? " without gaps" :\r
+ ""));\r
return sq;\r
}\r
+\r
public SequenceGroup getSelectionGroup()\r
{\r
return selectionGroup;\r
public void setFont(Font f)\r
{\r
font = f;\r
- if(nullFrame == null)\r
+ if (nullFrame == null)\r
{\r
nullFrame = new java.awt.Frame();\r
nullFrame.addNotify();\r
setCharHeight(fm.getHeight());\r
charWidth = fm.charWidth('M');\r
\r
- if(upperCasebold)\r
+ if (upperCasebold)\r
{\r
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());\r
fm = nullFrame.getGraphics().getFontMetrics(f2);\r
public void setHiddenColumns(ColumnSelection colsel)\r
{\r
this.colSel = colsel;\r
- if(colSel.getHiddenColumns()!=null)\r
+ if (colSel.getHiddenColumns() != null)\r
+ {\r
hasHiddenColumns = true;\r
+ }\r
}\r
\r
public ColumnSelection getColumnSelection()\r
{\r
ignoreGapsInConsensusCalculation = b;\r
updateConsensus(null);\r
- if (globalColourScheme!=null)\r
+ if (globalColourScheme != null)\r
{\r
globalColourScheme.setThreshold(globalColourScheme.getThreshold(),\r
- ignoreGapsInConsensusCalculation);\r
+ ignoreGapsInConsensusCalculation);\r
\r
}\r
}\r
public void addPropertyChangeListener(\r
java.beans.PropertyChangeListener listener)\r
{\r
- changeSupport.addPropertyChangeListener(listener);\r
+ changeSupport.addPropertyChangeListener(listener);\r
}\r
\r
/**\r
public void removePropertyChangeListener(\r
java.beans.PropertyChangeListener listener)\r
{\r
- changeSupport.removePropertyChangeListener(listener);\r
+ changeSupport.removePropertyChangeListener(listener);\r
}\r
\r
/**\r
*/\r
public void firePropertyChange(String prop, Object oldvalue, Object newvalue)\r
{\r
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
}\r
\r
-\r
-\r
public boolean getIgnoreGapsConsensus()\r
{\r
return ignoreGapsInConsensusCalculation;\r
}\r
+\r
public void hideSelectedColumns()\r
{\r
if (colSel.size() < 1)\r
+ {\r
return;\r
+ }\r
\r
colSel.hideSelectedColumns();\r
setSelectionGroup(null);\r
for (int i = 0; i < alignment.getWidth(); i++)\r
{\r
if (colSel.contains(i))\r
+ {\r
colSel.removeElement(i);\r
+ }\r
else\r
{\r
if (!hasHiddenColumns || colSel.isVisible(i))\r
}\r
}\r
\r
-\r
public void hideColumns(int start, int end)\r
{\r
- if(start==end)\r
+ if (start == end)\r
+ {\r
colSel.hideColumns(start);\r
+ }\r
else\r
+ {\r
colSel.hideColumns(start, end);\r
+ }\r
\r
hasHiddenColumns = true;\r
}\r
public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)\r
{\r
int sSize = sg.getSize();\r
- if(sSize < 2)\r
+ if (sSize < 2)\r
+ {\r
return;\r
+ }\r
\r
- if(hiddenRepSequences==null)\r
+ if (hiddenRepSequences == null)\r
+ {\r
hiddenRepSequences = new Hashtable();\r
+ }\r
\r
- hiddenRepSequences.put(repSequence, sg);\r
+ hiddenRepSequences.put(repSequence, sg);\r
\r
//Hide all sequences except the repSequence\r
- SequenceI [] seqs = new SequenceI[sSize-1];\r
+ SequenceI[] seqs = new SequenceI[sSize - 1];\r
int index = 0;\r
- for(int i=0; i<sSize; i++)\r
- if(sg.getSequenceAt(i)!=repSequence)\r
+ for (int i = 0; i < sSize; i++)\r
+ {\r
+ if (sg.getSequenceAt(i) != repSequence)\r
{\r
- if(index==sSize-1)\r
+ if (index == sSize - 1)\r
+ {\r
return;\r
+ }\r
\r
seqs[index++] = sg.getSequenceAt(i);\r
}\r
+ }\r
\r
hideSequence(seqs);\r
\r
- }\r
+ }\r
\r
public void hideAllSelectedSeqs()\r
{\r
if (selectionGroup == null)\r
+ {\r
return;\r
+ }\r
\r
SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);\r
\r
setSelectionGroup(null);\r
}\r
\r
- public void hideSequence(SequenceI [] seq)\r
+ public void hideSequence(SequenceI[] seq)\r
{\r
- if(seq!=null)\r
+ if (seq != null)\r
{\r
for (int i = 0; i < seq.length; i++)\r
+ {\r
alignment.getHiddenSequences().hideSequence(seq[i]);\r
+ }\r
\r
hasHiddenRows = true;\r
firePropertyChange("alignment", null, alignment.getSequences());\r
public void showColumn(int col)\r
{\r
colSel.revealHiddenColumns(col);\r
- if(colSel.getHiddenColumns()==null)\r
+ if (colSel.getHiddenColumns() == null)\r
+ {\r
hasHiddenColumns = false;\r
+ }\r
}\r
\r
public void showAllHiddenColumns()\r
\r
public void showAllHiddenSeqs()\r
{\r
- if(alignment.getHiddenSequences().getSize()>0)\r
+ if (alignment.getHiddenSequences().getSize() > 0)\r
{\r
- if(selectionGroup==null)\r
+ if (selectionGroup == null)\r
{\r
selectionGroup = new SequenceGroup();\r
- selectionGroup.setEndRes(alignment.getWidth()-1);\r
+ selectionGroup.setEndRes(alignment.getWidth() - 1);\r
}\r
Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);\r
- for(int t=0; t<tmp.size(); t++)\r
+ for (int t = 0; t < tmp.size(); t++)\r
{\r
selectionGroup.addSequence(\r
- (SequenceI)tmp.elementAt(t), false\r
+ (SequenceI) tmp.elementAt(t), false\r
);\r
}\r
firePropertyChange("alignment", null, alignment.getSequences());\r
hasHiddenRows = false;\r
hiddenRepSequences = null;\r
- }\r
+ }\r
}\r
\r
public int adjustForHiddenSeqs(int alignmentIndex)\r
SequenceI[] sequences;\r
\r
if (selectionGroup == null)\r
+ {\r
sequences = alignment.getSequencesArray();\r
+ }\r
else\r
+ {\r
sequences = selectionGroup.getSelectionAsNewSequences(alignment);\r
+ }\r
\r
return sequences;\r
}\r
* which contain hidden columns.\r
* @return String[]\r
*/\r
- public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)\r
+ public jalview.datamodel.CigarArray getViewAsCigars(boolean\r
+ selectedRegionOnly)\r
{\r
- CigarArray selection=null;\r
- SequenceI [] seqs= null;\r
+ CigarArray selection = null;\r
+ SequenceI[] seqs = null;\r
int i, iSize;\r
int start = 0, end = 0;\r
- if(selectedRegionOnly && selectionGroup!=null)\r
+ if (selectedRegionOnly && selectionGroup != null)\r
{\r
iSize = selectionGroup.getSize();\r
seqs = selectionGroup.getSequencesInOrder(alignment);\r
{\r
iSize = alignment.getHeight();\r
seqs = alignment.getSequencesArray();\r
- end = alignment.getWidth()-1;\r
+ end = alignment.getWidth() - 1;\r
}\r
SeqCigar[] selseqs = new SeqCigar[iSize];\r
- for(i=0; i<iSize; i++)\r
+ for (i = 0; i < iSize; i++)\r
{\r
selseqs[i] = new SeqCigar(seqs[i], start, end);\r
}\r
- selection=new CigarArray(selseqs);\r
+ selection = new CigarArray(selseqs);\r
// now construct the CigarArray operations\r
- if (hasHiddenColumns) {\r
+ if (hasHiddenColumns)\r
+ {\r
Vector regions = colSel.getHiddenColumns();\r
- int [] region;\r
+ int[] region;\r
int hideStart, hideEnd;\r
- int last=start;\r
- for (int j = 0; last<end & j < regions.size(); j++)\r
+ int last = start;\r
+ for (int j = 0; last < end & j < regions.size(); j++)\r
{\r
region = (int[]) regions.elementAt(j);\r
hideStart = region[0];\r
hideEnd = region[1];\r
// edit hidden regions to selection range\r
- if(hideStart<last) {\r
+ if (hideStart < last)\r
+ {\r
if (hideEnd > last)\r
{\r
hideStart = last;\r
- } else\r
+ }\r
+ else\r
+ {\r
continue;\r
+ }\r
}\r
\r
- if (hideStart>end)\r
+ if (hideStart > end)\r
+ {\r
break;\r
+ }\r
\r
- if (hideEnd>end)\r
- hideEnd=end;\r
+ if (hideEnd > end)\r
+ {\r
+ hideEnd = end;\r
+ }\r
\r
- if (hideStart>hideEnd)\r
+ if (hideStart > hideEnd)\r
+ {\r
break;\r
+ }\r
/**\r
* form operations...\r
*/\r
- if (last<hideStart)\r
- selection.addOperation(CigarArray.M, hideStart-last);\r
- selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);\r
- last = hideEnd+1;\r
+ if (last < hideStart)\r
+ {\r
+ selection.addOperation(CigarArray.M, hideStart - last);\r
+ }\r
+ selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);\r
+ last = hideEnd + 1;\r
}\r
// Final match if necessary.\r
- if (last<end)\r
- selection.addOperation(CigarArray.M, end-last+1);\r
- } else {\r
- selection.addOperation(CigarArray.M, end-start+1);\r
+ if (last < end)\r
+ {\r
+ selection.addOperation(CigarArray.M, end - last + 1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ selection.addOperation(CigarArray.M, end - start + 1);\r
}\r
return selection;\r
}\r
+\r
/**\r
* return a compact representation of the current alignment selection to\r
* pass to an analysis function\r
* @param selectedOnly boolean true to just return the selected view\r
* @return AlignmentView\r
*/\r
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {\r
+ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)\r
+ {\r
// JBPNote:\r
// this is here because the AlignmentView constructor modifies the CigarArray\r
// object. Refactoring of Cigar and alignment view representation should\r
// be done to remove redundancy.\r
CigarArray aligview = getViewAsCigars(selectedOnly);\r
- if (aligview!=null) {\r
+ if (aligview != null)\r
+ {\r
return new AlignmentView(aligview,\r
- (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);\r
+ (selectedOnly && selectionGroup != null) ?\r
+ selectionGroup.getStartRes() : 0);\r
}\r
return null;\r
}\r
+\r
/**\r
* This method returns the visible alignment as text, as\r
* seen on the GUI, ie if columns are hidden they will not\r
* which contain hidden columns.\r
* @return String[]\r
*/\r
- public String [] getViewAsString(boolean selectedRegionOnly)\r
+ public String[] getViewAsString(boolean selectedRegionOnly)\r
{\r
- String [] selection = null;\r
- SequenceI [] seqs= null;\r
+ String[] selection = null;\r
+ SequenceI[] seqs = null;\r
int i, iSize;\r
int start = 0, end = 0;\r
- if(selectedRegionOnly && selectionGroup!=null)\r
+ if (selectedRegionOnly && selectionGroup != null)\r
{\r
iSize = selectionGroup.getSize();\r
seqs = selectionGroup.getSequencesInOrder(alignment);\r
start = selectionGroup.getStartRes();\r
- end = selectionGroup.getEndRes()+1;\r
+ end = selectionGroup.getEndRes() + 1;\r
}\r
else\r
{\r
\r
selection = new String[iSize];\r
\r
-\r
- for(i=0; i<iSize; i++)\r
+ for (i = 0; i < iSize; i++)\r
{\r
if (hasHiddenColumns)\r
{\r
- StringBuffer visibleSeq = new StringBuffer();\r
- Vector regions = colSel.getHiddenColumns();\r
-\r
- int blockStart = start, blockEnd=end;\r
- int [] region;\r
- int hideStart, hideEnd;\r
+ StringBuffer visibleSeq = new StringBuffer();\r
+ Vector regions = colSel.getHiddenColumns();\r
\r
- for (int j = 0; j < regions.size(); j++)\r
- {\r
- region = (int[]) regions.elementAt(j);\r
- hideStart = region[0];\r
- hideEnd = region[1];\r
+ int blockStart = start, blockEnd = end;\r
+ int[] region;\r
+ int hideStart, hideEnd;\r
\r
- if(hideStart < start)\r
- {\r
- continue;\r
- }\r
+ for (int j = 0; j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
\r
- blockStart = Math.min(blockStart, hideEnd+1);\r
- blockEnd = Math.min(blockEnd, hideStart);\r
+ if (hideStart < start)\r
+ {\r
+ continue;\r
+ }\r
\r
- if(blockStart>blockEnd)\r
- {\r
- break;\r
- }\r
+ blockStart = Math.min(blockStart, hideEnd + 1);\r
+ blockEnd = Math.min(blockEnd, hideStart);\r
\r
+ if (blockStart > blockEnd)\r
+ {\r
+ break;\r
+ }\r
\r
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));\r
\r
- blockStart = hideEnd+1;\r
- blockEnd = end;\r
- }\r
+ blockStart = hideEnd + 1;\r
+ blockEnd = end;\r
+ }\r
\r
- if(end>blockStart)\r
- visibleSeq.append(seqs[i].getSequence(blockStart, end));\r
+ if (end > blockStart)\r
+ {\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));\r
+ }\r
\r
- selection[i] = visibleSeq.toString();\r
+ selection[i] = visibleSeq.toString();\r
}\r
else\r
{\r
public Color getSequenceColour(SequenceI seq)\r
{\r
if (sequenceColours == null || !sequenceColours.containsKey(seq))\r
+ {\r
return Color.white;\r
+ }\r
else\r
+ {\r
return (Color) sequenceColours.get(seq);\r
+ }\r
}\r
\r
public void setSequenceColour(SequenceI seq, Color col)\r
{\r
if (sequenceColours == null)\r
+ {\r
sequenceColours = new Hashtable();\r
+ }\r
\r
if (col == null)\r
+ {\r
sequenceColours.remove(seq);\r
+ }\r
else\r
+ {\r
sequenceColours.put(seq, col);\r
+ }\r
}\r
\r
public String getSequenceSetId()\r
{\r
if (sequenceSetID == null)\r
+ {\r
sequenceSetID = alignment.hashCode() + "";\r
+ }\r
\r
return sequenceSetID;\r
}\r
//Reset endRes of groups if beyond alignment width\r
int alWidth = alignment.getWidth();\r
Vector groups = alignment.getGroups();\r
- if(groups!=null)\r
+ if (groups != null)\r
{\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
- if(sg.getEndRes()>alWidth)\r
- sg.setEndRes(alWidth-1);\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+ if (sg.getEndRes() > alWidth)\r
+ {\r
+ sg.setEndRes(alWidth - 1);\r
+ }\r
}\r
}\r
\r
- if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)\r
- selectionGroup.setEndRes(alWidth-1);\r
+ if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)\r
+ {\r
+ selectionGroup.setEndRes(alWidth - 1);\r
+ }\r
\r
resetAllColourSchemes();\r
\r
- //AW alignment.adjustSequenceAnnotations();\r
+ //AW alignment.adjustSequenceAnnotations();\r
}\r
\r
void resetAllColourSchemes()\r
{\r
ColourSchemeI cs = globalColourScheme;\r
- if(cs!=null)\r
+ if (cs != null)\r
{\r
if (cs instanceof ClustalxColourScheme)\r
{\r
}\r
\r
int s, sSize = alignment.getGroups().size();\r
- for(s=0; s<sSize; s++)\r
+ for (s = 0; s < sSize; s++)\r
{\r
- SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);\r
- if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
+ SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);\r
+ if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(\r
+ ( (ClustalxColourScheme) sg.cs).resetClustalX(\r
sg.getSequences(hiddenRepSequences), sg.getWidth());\r
}\r
sg.recalcConservation();\r
}\r
}\r
\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff