X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=4fd39a3d6e86290f371fb8210c5c99d6d8a1d49c;hb=04bb62b586382f183f08eb70131e7bf5f67cb47a;hp=904e1e2d05bda4359742efa1b52566e57505cbb1;hpb=ba2255324de03f4f66ed1883c105404c4c97c66b;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 904e1e2..4fd39a3 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1,4 +1,4 @@ -/* + /* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * @@ -43,7 +43,8 @@ public class AlignViewport int endRes; int startSeq; int endSeq; - boolean showFullId = false; + boolean showDBPrefix = true; + boolean showJVSuffix = true; boolean showText = true; boolean showColourText = false; boolean showBoxes = true; @@ -61,8 +62,7 @@ public class AlignViewport SequenceGroup selectionGroup; int charHeight; int charWidth; - int chunkWidth; - int chunkHeight; + int wrappedWidth; Font font = new Font("SansSerif", Font.PLAIN, 10); AlignmentI alignment; ColumnSelection colSel = new ColumnSelection(); @@ -85,6 +85,17 @@ public class AlignViewport // JBPNote Prolly only need this in the applet version. private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this); + boolean ignoreGapsInConsensusCalculation = false; + + boolean isDataset = false; + + + public AlignViewport(AlignmentI al, boolean dataset) + { + isDataset = dataset; + setAlignment(al); + init(); + } /** * Creates a new AlignViewport object. * @@ -93,65 +104,62 @@ public class AlignViewport public AlignViewport(AlignmentI al) { setAlignment(al); + init(); + } + + void init() + { this.startRes = 0; - this.endRes = al.getWidth() - 1; + this.endRes = alignment.getWidth() - 1; this.startSeq = 0; - this.endSeq = al.getHeight() - 1; + this.endSeq = alignment.getHeight() - 1; - updateFromPreferences(); - } + showDBPrefix = Cache.getDefault("SHOW_DBPREFIX", true); + showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); + showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); + showConservation = Cache.getDefault("SHOW_CONSERVATION", true); - /** - * DOCUMENT ME! - */ - public void updateFromPreferences() - { - showFullId = Preferences.showFullId; - showAnnotation = Preferences.showAnnotation; - showConservation = Preferences.showConservation; - showQuality = Preferences.showQuality; - showIdentity = Preferences.showIdentity; - showFullId = Preferences.showFullId; + showQuality = Cache.getDefault("SHOW_QUALITY", true); + showIdentity = Cache.getDefault("SHOW_IDENTITY", true); - String fontName = Preferences.fontName; - String fontStyle = Preferences.fontStyle; - String fontSize = Cache.getProperty("FONT_SIZE"); + String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); + String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ; + String fontSize = Cache.getDefault("FONT_SIZE", "10"); - if ((fontName != null) && (fontStyle != null) && (fontSize != null)) - { - int style = 0; + int style = 0; - if (fontStyle.equals("bold")) - { - style = 1; - } - else if (fontStyle.equals("italic")) - { - style = 2; - } + if (fontStyle.equals("bold")) + { + style = 1; + } + else if (fontStyle.equals("italic")) + { + style = 2; + } - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - } - else - { - setFont(font); - } + setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + + + alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) ); - alignment.setGapCharacter(Preferences.gapSymbol); // We must set conservation and consensus before setting colour, // as Blosum and Clustal require this to be done - updateConservation(); - updateConsensus(); + if(vconsensus==null && !isDataset) + { + updateConservation(); + updateConsensus(); + } - if (Preferences.defaultColour != null) + if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) { - globalColourScheme = ColourSchemeProperty.getColour(alignment, - Preferences.defaultColour); + globalColourScheme = ColourSchemeProperty.getColour(alignment, + jalview.bin.Cache.getProperty("DEFAULT_COLOUR")); if (globalColourScheme instanceof UserColourScheme) { globalColourScheme = UserDefinedColours.loadDefaultColours(); + ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus()); } if (globalColourScheme != null) @@ -161,6 +169,8 @@ public class AlignViewport } } + + /** * DOCUMENT ME! * @@ -176,9 +186,13 @@ public class AlignViewport */ public void updateConservation() { + if(alignment.isNucleotide()) + return; + + try{ Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alignment.getWidth() - 1); + jalview.schemes.ResidueProperties.propHash, 3, + alignment.getSequences(), 0, alignment.getWidth() - 1); cons.calculate(); cons.verdict(false, ConsPercGaps); cons.findQuality(); @@ -207,71 +221,89 @@ public class AlignViewport for (int i = 0; i < alWidth; i++) { - float value = 0; - - try + float value = 0; + + try + { + value = Integer.parseInt(sequence.charAt(i) + ""); + } + catch (Exception ex) + { + if (sequence.charAt(i) == '*') { - value = Integer.parseInt(sequence.charAt(i) + ""); + value = 11; } - catch (Exception ex) - { - if (sequence.charAt(i) == '*') - { - value = 11; - } - if (sequence.charAt(i) == '+') - { - value = 10; - } + if (sequence.charAt(i) == '+') + { + value = 10; } - - float vprop = value - min; - vprop /= max; - annotations[i] = new Annotation(sequence.charAt(i) + "", - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), minG + (maxG * vprop), - minB + (maxB * vprop))); - - // Quality calc - value = ((Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - qannotations[i] = new Annotation(" ", String.valueOf(value), ' ', - value, - new Color(minR + (maxR * vprop), minG + (maxG * vprop), - minB + (maxB * vprop))); + } + + float vprop = value - min; + vprop /= max; + annotations[i] = new Annotation(sequence.charAt(i) + "", + String.valueOf(value), ' ', value, + new Color(minR + (maxR * vprop), + minG + (maxG * vprop), + minB + (maxB * vprop))); + + // Quality calc + value = ( (Double) cons.quality.get(i)).floatValue(); + vprop = value - qmin; + vprop /= qmax; + qannotations[i] = new Annotation(" ", String.valueOf(value), ' ', + value, + new Color(minR + (maxR * vprop), + minG + (maxG * vprop), + minB + (maxB * vprop))); } if (conservation == null) { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", annotations, 0f, // cons.qualityRange[0].floatValue(), - 11f, // cons.qualityRange[1].floatValue() - 1); - - if (showConservation) - { - alignment.addAnnotation(conservation); - } - - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), 1); - - if (showQuality) - { - alignment.addAnnotation(quality); - } + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + + ConsPercGaps + "% gaps", + annotations, 0f, // cons.qualityRange[0].floatValue(), + 11f, // cons.qualityRange[1].floatValue() + 1); + + if (showConservation) + { + alignment.addAnnotation(conservation); + } + + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + qannotations, + cons.qualityRange[0].floatValue(), + cons.qualityRange[1].floatValue(), + 1); + + if (showQuality) + { + alignment.addAnnotation(quality); + } } else { - conservation.annotations = annotations; - quality.annotations = qannotations; - quality.graphMax = cons.qualityRange[1].floatValue(); + conservation.annotations = annotations; + quality.annotations = qannotations; + quality.graphMax = cons.qualityRange[1].floatValue(); } + } + catch (OutOfMemoryError error) + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Out of memory calculating conservation!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + System.out.println("Conservation calculation: " + error); + System.gc(); + + } } /** @@ -279,6 +311,7 @@ public class AlignViewport */ public void updateConsensus() { + try{ Annotation[] annotations = new Annotation[alignment.getWidth()]; // this routine prevents vconsensus becoming a new object each time @@ -286,59 +319,76 @@ public class AlignViewport // and PID colouring of alignment if (vconsensus == null) { - vconsensus = alignment.getAAFrequency(); + vconsensus = alignment.getAAFrequency(); } else { - Vector temp = alignment.getAAFrequency(); - vconsensus.clear(); + Vector temp = alignment.getAAFrequency(); + vconsensus.clear(); - Enumeration e = temp.elements(); + Enumeration e = temp.elements(); - while (e.hasMoreElements()) - { - vconsensus.add(e.nextElement()); - } + while (e.hasMoreElements()) + { + vconsensus.add(e.nextElement()); + } } Hashtable hash = null; for (int i = 0; i < alignment.getWidth(); i++) { - hash = (Hashtable) vconsensus.elementAt(i); + hash = (Hashtable) vconsensus.elementAt(i); - float value = Float.parseFloat(hash.get("maxCount").toString()); - value /= Float.parseFloat(hash.get("size").toString()); + float value = 0; + if (ignoreGapsInConsensusCalculation) + value = ( (Float) hash.get("pid_nogaps")).floatValue(); + else + value = ( (Float) hash.get("pid_gaps")).floatValue(); - value *= 100; + String maxRes = hash.get("maxResidue").toString(); + String mouseOver = hash.get("maxResidue") + " "; - String maxRes = hash.get("maxResidue") + " "; - String mouseOver = hash.get("maxResidue") + " "; + if (maxRes.length() > 1) + { + mouseOver = "[" + maxRes + "] "; + maxRes = "+"; + } - if (maxRes.length() > 2) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+ "; - } - - mouseOver += ((int) value + "%"); - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); + mouseOver += ( (int) value + "%"); + annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); } if (consensus == null) { - consensus = new AlignmentAnnotation("Consensus", "PID", - annotations, 0f, 100f, 1); + consensus = new AlignmentAnnotation("Consensus", "PID", + annotations, 0f, 100f, 1); - if (showIdentity) - { - alignment.addAnnotation(consensus); - } + if (showIdentity) + { + alignment.addAnnotation(consensus); + } } else { - consensus.annotations = annotations; + consensus.annotations = annotations; } + + if (globalColourScheme != null) + globalColourScheme.setConsensus(vconsensus); + + }catch(OutOfMemoryError error) + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Out of memory calculating consensus!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + System.out.println("Consensus calculation: " + error); + System.gc(); + } + } /** @@ -593,9 +643,9 @@ public class AlignViewport * * @param w DOCUMENT ME! */ - public void setChunkWidth(int w) + public void setWrappedWidth(int w) { - this.chunkWidth = w; + this.wrappedWidth = w; } /** @@ -603,30 +653,11 @@ public class AlignViewport * * @return DOCUMENT ME! */ - public int getChunkWidth() + public int getWrappedWidth() { - return chunkWidth; + return wrappedWidth; } - /** - * DOCUMENT ME! - * - * @param h DOCUMENT ME! - */ - public void setChunkHeight(int h) - { - this.chunkHeight = h; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getChunkHeight() - { - return chunkHeight; - } /** * DOCUMENT ME! @@ -847,15 +878,6 @@ public class AlignViewport return colSel; } - /** - * DOCUMENT ME! - * - * @param height DOCUMENT ME! - */ - public void resetSeqLimits(int height) - { - setEndSeq(height / getCharHeight()); - } /** * DOCUMENT ME! @@ -902,9 +924,9 @@ public class AlignViewport * * @return DOCUMENT ME! */ - public boolean getShowFullId() + public boolean getShowJVSuffix() { - return showFullId; + return showJVSuffix; } /** @@ -912,9 +934,29 @@ public class AlignViewport * * @param b DOCUMENT ME! */ - public void setShowFullId(boolean b) + public void setShowJVSuffix(boolean b) { - showFullId = b; + showJVSuffix = b; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public boolean getShowDBPrefix() + { + return showDBPrefix; + } + + /** + * DOCUMENT ME! + * + * @param b DOCUMENT ME! + */ + public void setShowDBPrefix(boolean b) + { + showDBPrefix = b; } /** @@ -998,7 +1040,7 @@ public class AlignViewport } /** - * DOCUMENT ME! + * Property change listener for changes in alignment * * @param listener DOCUMENT ME! */ @@ -1020,7 +1062,7 @@ public class AlignViewport } /** - * DOCUMENT ME! + * Property change listener for changes in alignment * * @param prop DOCUMENT ME! * @param oldvalue DOCUMENT ME! @@ -1030,4 +1072,30 @@ public class AlignViewport { changeSupport.firePropertyChange(prop, oldvalue, newvalue); } + + public void setIgnoreGapsConsensus(boolean b) + { + ignoreGapsInConsensusCalculation = b; + updateConsensus(); + if(globalColourScheme!=null) + { + globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation); + } + + } + + public boolean getIgnoreGapsConsensus() + { + return ignoreGapsInConsensusCalculation; + } + + public void setDataset(boolean b) + { + isDataset = b; + } + + public boolean isDataset() + { + return isDataset; + } }