-/*\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
int endRes;\r
int startSeq;\r
int endSeq;\r
- boolean showFullId = false;\r
+ boolean showJVSuffix = true;\r
boolean showText = true;\r
boolean showColourText = false;\r
boolean showBoxes = true;\r
SequenceGroup selectionGroup;\r
int charHeight;\r
int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
- Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ boolean validCharWidth;\r
+ int wrappedWidth;\r
+ Font font;\r
AlignmentI alignment;\r
ColumnSelection colSel = new ColumnSelection();\r
int threshold;\r
boolean scaleAboveWrapped = false;\r
boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
+ boolean hasHiddenColumns = false;\r
+ boolean hasHiddenRows = false;\r
+\r
+ boolean cursorMode = false;\r
+\r
+ // The following vector holds the features which are\r
+ // currently visible, in the correct order or rendering\r
+ Hashtable featuresDisplayed = null;\r
+\r
\r
/** DOCUMENT ME!! */\r
public Vector vconsensus;\r
AlignmentAnnotation consensus;\r
AlignmentAnnotation conservation;\r
AlignmentAnnotation quality;\r
+ boolean autoCalculateConsensus = true;\r
\r
/** DOCUMENT ME!! */\r
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
+ boolean isDataset = false;\r
+\r
+ boolean antiAlias = false;\r
+\r
+ boolean padGaps = false;\r
+\r
+\r
+ public AlignViewport(AlignmentI al, boolean dataset)\r
+ {\r
+ isDataset = dataset;\r
+ setAlignment(al);\r
+ init();\r
+ }\r
/**\r
* Creates a new AlignViewport object.\r
*\r
public AlignViewport(AlignmentI al)\r
{\r
setAlignment(al);\r
+ init();\r
+ }\r
+\r
+ void init()\r
+ {\r
this.startRes = 0;\r
- this.endRes = al.getWidth() - 1;\r
+ this.endRes = alignment.getWidth() - 1;\r
this.startSeq = 0;\r
- this.endSeq = al.getHeight() - 1;\r
+ this.endSeq = alignment.getHeight() - 1;\r
\r
- updateFromPreferences();\r
- }\r
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateFromPreferences()\r
- {\r
- showFullId = Cache.getDefault("SHOW_FULL_ID", true);\r
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
\r
showQuality = Cache.getDefault("SHOW_QUALITY", true);\r
showIdentity = Cache.getDefault("SHOW_IDENTITY", true);\r
\r
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);\r
+\r
+ padGaps = Cache.getDefault("PAD_GAPS", false);\r
+\r
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");\r
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;\r
String fontSize = Cache.getDefault("FONT_SIZE", "10");\r
\r
// We must set conservation and consensus before setting colour,\r
// as Blosum and Clustal require this to be done\r
- updateConservation();\r
- updateConsensus();\r
+ if(vconsensus==null && !isDataset)\r
+ {\r
+ updateConservation();\r
+ updateConsensus();\r
+ }\r
\r
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
{\r
*\r
* @param b DOCUMENT ME!\r
*/\r
- public void showSequenceFeatures(boolean b)\r
+ public void setShowSequenceFeatures(boolean b)\r
{\r
showSequenceFeatures = b;\r
}\r
\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
+ return showSequenceFeatures;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*/\r
public void updateConservation()\r
{\r
+ if(alignment.isNucleotide())\r
+ return;\r
+\r
+ try{\r
Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0, alignment.getWidth() - 1);\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
+ alignment.getSequences(), 0, alignment.getWidth() - 1);\r
cons.calculate();\r
cons.verdict(false, ConsPercGaps);\r
cons.findQuality();\r
\r
for (int i = 0; i < alWidth; i++)\r
{\r
- float value = 0;\r
-\r
- try\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
- value = 11;\r
- }\r
\r
- if (sequence.charAt(i) == '+')\r
- {\r
- value = 10;\r
- }\r
+ if (sequence.charAt(i) == '+')\r
+ {\r
+ value = 10;\r
}\r
-\r
- float vprop = value - min;\r
- vprop /= max;\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- String.valueOf(value), ' ', value,\r
- new Color(minR + (maxR * vprop), minG + (maxG * vprop),\r
- minB + (maxB * vprop)));\r
-\r
- // Quality calc\r
- value = ((Double) cons.quality.get(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop /= qmax;\r
- qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
- value,\r
- new Color(minR + (maxR * vprop), minG + (maxG * vprop),\r
- minB + (maxB * vprop)));\r
+ }\r
+\r
+ float vprop = value - min;\r
+ vprop /= max;\r
+ annotations[i] = new Annotation(sequence.charAt(i) + "",\r
+ String.valueOf(value), ' ', 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
+ vprop = value - qmin;\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
{\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than " +\r
- ConsPercGaps + "% gaps", annotations, 0f, // cons.qualityRange[0].floatValue(),\r
- 11f, // cons.qualityRange[1].floatValue()\r
- 1);\r
-\r
- if (showConservation)\r
- {\r
- alignment.addAnnotation(conservation);\r
- }\r
-\r
- quality = new AlignmentAnnotation("Quality",\r
- "Alignment Quality based on Blosum62 scores", qannotations,\r
- cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(), 1);\r
-\r
- if (showQuality)\r
- {\r
- alignment.addAnnotation(quality);\r
- }\r
+ conservation = new AlignmentAnnotation("Conservation",\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
+ annotations, 0f, // cons.qualityRange[0].floatValue(),\r
+ 11f, // cons.qualityRange[1].floatValue()\r
+ AlignmentAnnotation.BAR_GRAPH);\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
+ AlignmentAnnotation.BAR_GRAPH);\r
+\r
+ if (showQuality)\r
+ {\r
+ alignment.addAnnotation(quality);\r
+ }\r
}\r
else\r
{\r
- conservation.annotations = annotations;\r
- quality.annotations = qannotations;\r
- quality.graphMax = cons.qualityRange[1].floatValue();\r
+ conservation.annotations = annotations;\r
+ quality.annotations = qannotations;\r
+ quality.graphMax = cons.qualityRange[1].floatValue();\r
}\r
+ }\r
+ catch (OutOfMemoryError error)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory calculating conservation!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+\r
+ System.out.println("Conservation calculation: " + error);\r
+ System.gc();\r
+\r
+ }\r
}\r
\r
/**\r
*/\r
public void updateConsensus()\r
{\r
+ try{\r
Annotation[] annotations = new Annotation[alignment.getWidth()];\r
\r
// this routine prevents vconsensus becoming a new object each time\r
// and PID colouring of alignment\r
if (vconsensus == null)\r
{\r
- vconsensus = alignment.getAAFrequency();\r
+ vconsensus = alignment.getAAFrequency();\r
}\r
else\r
{\r
- Vector temp = alignment.getAAFrequency();\r
- vconsensus.clear();\r
+ Vector temp = alignment.getAAFrequency();\r
+ vconsensus.clear();\r
\r
- Enumeration e = temp.elements();\r
+ Enumeration e = temp.elements();\r
\r
- while (e.hasMoreElements())\r
- {\r
- vconsensus.add(e.nextElement());\r
- }\r
+ while (e.hasMoreElements())\r
+ {\r
+ vconsensus.add(e.nextElement());\r
+ }\r
}\r
\r
Hashtable hash = null;\r
\r
for (int i = 0; i < alignment.getWidth(); i++)\r
{\r
- hash = (Hashtable) vconsensus.elementAt(i);\r
+ hash = (Hashtable) vconsensus.elementAt(i);\r
\r
- float value = 0;\r
- if(ignoreGapsInConsensusCalculation)\r
- value = ((Float)hash.get("pid_nogaps")).floatValue();\r
- else\r
- value = ((Float)hash.get("pid_gaps")).floatValue();\r
+ float value = 0;\r
+ if (ignoreGapsInConsensusCalculation)\r
+ value = ( (Float) hash.get("pid_nogaps")).floatValue();\r
+ else\r
+ value = ( (Float) hash.get("pid_gaps")).floatValue();\r
\r
- String maxRes = hash.get("maxResidue").toString();\r
- String mouseOver = hash.get("maxResidue")+" ";\r
+ String maxRes = hash.get("maxResidue").toString();\r
+ String mouseOver = hash.get("maxResidue") + " ";\r
\r
- if (maxRes.length() > 1)\r
- {\r
- mouseOver = "[" + maxRes + "] ";\r
- maxRes = "+";\r
- }\r
+ if (maxRes.length() > 1)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+";\r
+ }\r
\r
- mouseOver += ((int) value + "%");\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ mouseOver += ( (int) value + "%");\r
+ annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
}\r
\r
if (consensus == null)\r
{\r
- consensus = new AlignmentAnnotation("Consensus", "PID",\r
- annotations, 0f, 100f, 1);\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);\r
\r
- if (showIdentity)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
+ if (showIdentity)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
}\r
else\r
{\r
- consensus.annotations = annotations;\r
+ consensus.annotations = annotations;\r
}\r
\r
- if(globalColourScheme!=null)\r
+ if (globalColourScheme != null)\r
globalColourScheme.setConsensus(vconsensus);\r
+\r
+ }catch(OutOfMemoryError error)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory calc45ulating consensus!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+\r
+\r
+ System.out.println("Consensus calculation: " + error);\r
+ System.gc();\r
+ }\r
+\r
}\r
\r
/**\r
java.awt.FontMetrics fm = c.getFontMetrics(font);\r
setCharHeight(fm.getHeight());\r
setCharWidth(fm.charWidth('M'));\r
+ validCharWidth = true;\r
}\r
\r
/**\r
*\r
* @param w DOCUMENT ME!\r
*/\r
- public void setChunkWidth(int w)\r
+ public void setWrappedWidth(int w)\r
{\r
- this.chunkWidth = w;\r
+ this.wrappedWidth = w;\r
}\r
\r
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public int getChunkWidth()\r
+ public int getWrappedWidth()\r
{\r
- return chunkWidth;\r
+ return wrappedWidth;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param h DOCUMENT ME!\r
- */\r
- public void setChunkHeight(int h)\r
- {\r
- this.chunkHeight = h;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getChunkHeight()\r
- {\r
- return chunkHeight;\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
return colSel;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param height DOCUMENT ME!\r
- */\r
- public void resetSeqLimits(int height)\r
- {\r
- setEndSeq(height / getCharHeight());\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public boolean getShowFullId()\r
+ public boolean getShowJVSuffix()\r
{\r
- return showFullId;\r
+ return showJVSuffix;\r
}\r
\r
/**\r
*\r
* @param b DOCUMENT ME!\r
*/\r
- public void setShowFullId(boolean b)\r
+ public void setShowJVSuffix(boolean b)\r
{\r
- showFullId = b;\r
+ showJVSuffix = b;\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
}\r
\r
/**\r
- * DOCUMENT ME!\r
+ * Property change listener for changes in alignment\r
*\r
* @param listener DOCUMENT ME!\r
*/\r
}\r
\r
/**\r
- * DOCUMENT ME!\r
+ * Property change listener for changes in alignment\r
*\r
* @param prop DOCUMENT ME!\r
* @param oldvalue DOCUMENT ME!\r
{\r
ignoreGapsInConsensusCalculation = b;\r
updateConsensus();\r
- if(globalColourScheme!=null && globalColourScheme instanceof ResidueColourScheme)\r
+ if(globalColourScheme!=null)\r
{\r
- ((ResidueColourScheme) globalColourScheme).setThreshold(\r
- ((ResidueColourScheme) globalColourScheme).getThreshold(), ignoreGapsInConsensusCalculation);\r
-\r
-\r
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);\r
}\r
-\r
}\r
\r
public boolean getIgnoreGapsConsensus()\r
{\r
return ignoreGapsInConsensusCalculation;\r
}\r
+\r
+ public void setDataset(boolean b)\r
+ {\r
+ isDataset = b;\r
+ }\r
+\r
+ public boolean isDataset()\r
+ {\r
+ return isDataset;\r
+ }\r
+\r
+ public void hideSequence(SequenceI seq)\r
+ {\r
+ alignment.getHiddenSequences().hideSequence(seq);\r
+ hasHiddenRows = true;\r
+ }\r
+\r
+ public void showSequence(int index)\r
+ {\r
+ alignment.getHiddenSequences().showSequence(index);\r
+\r
+ if(alignment.getHiddenSequences().getSize()<1)\r
+ hasHiddenRows = false;\r
+ }\r
+\r
+ public int adjustForHiddenSeqs(int alignmentIndex)\r
+ {\r
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff