X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=b39aaebd45d4861f497aeee5fb981d8fe76ff61c;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=33a73d384af57e25cd84b894084bc39e234cf608;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 33a73d3..b39aaeb 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,22 +1,21 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.appletgui; import java.util.*; @@ -31,50 +30,73 @@ import jalview.schemes.*; public class AlignViewport { int startRes; + int endRes; int startSeq; + int endSeq; boolean cursorMode = false; boolean showJVSuffix = true; + boolean showText = true; + boolean showColourText = false; + boolean showBoxes = true; + boolean wrapAlignment = false; + boolean renderGaps = true; + boolean showSequenceFeatures = false; + boolean showAnnotation = true; + boolean showConservation = true; + boolean showQuality = true; + boolean showConsensus = true; + boolean upperCasebold = false; boolean colourAppliesToAllGroups = true; + ColourSchemeI globalColourScheme = null; + boolean conservationColourSelected = false; + boolean abovePIDThreshold = false; SequenceGroup selectionGroup; int charHeight; + int charWidth; + int wrappedWidth; Font font = new Font("SansSerif", Font.PLAIN, 10); + boolean validCharWidth = true; + AlignmentI alignment; ColumnSelection colSel = new ColumnSelection(); int threshold; + int increment; NJTree currentTree = null; boolean scaleAboveWrapped = true; + boolean scaleLeftWrapped = true; + boolean scaleRightWrapped = true; // The following vector holds the features which are @@ -82,20 +104,25 @@ public class AlignViewport public Hashtable featuresDisplayed; boolean hasHiddenColumns = false; + boolean hasHiddenRows = false; + boolean showHiddenMarkers = true; public Hashtable[] hconsensus; + AlignmentAnnotation consensus; + AlignmentAnnotation conservation; + AlignmentAnnotation quality; boolean autocalculateConsensus = true; public int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - private java.beans.PropertyChangeSupport changeSupport = new java.beans. - PropertyChangeSupport(this); + private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + this); boolean ignoreGapsInConsensusCalculation = false; @@ -106,6 +133,7 @@ public class AlignViewport boolean MAC = false; Stack historyList = new Stack(); + Stack redoList = new Stack(); String sequenceSetID; @@ -123,7 +151,7 @@ public class AlignViewport setFont(font); MAC = new jalview.util.Platform().isAMac(); - + if (applet != null) { String param = applet.getParameter("showFullId"); @@ -164,7 +192,6 @@ public class AlignViewport upperCasebold = true; } } - } @@ -183,7 +210,8 @@ public class AlignViewport if (colour != null) { - globalColourScheme = ColourSchemeProperty.getColour(alignment, colour); + globalColourScheme = ColourSchemeProperty.getColour(alignment, + colour); if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -192,8 +220,8 @@ public class AlignViewport if (applet.getParameter("userDefinedColour") != null) { - ( (UserColourScheme) globalColourScheme).parseAppletParameter( - applet.getParameter("userDefinedColour")); + ((UserColourScheme) globalColourScheme).parseAppletParameter(applet + .getParameter("userDefinedColour")); } } if (hconsensus == null) @@ -201,10 +229,8 @@ public class AlignViewport if (!alignment.isNucleotide()) { conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", - new Annotation[1], 0f, - 11f, + "Conservation of total alignment less than " + ConsPercGaps + + "% gaps", new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; @@ -218,10 +244,7 @@ public class AlignViewport { quality = new AlignmentAnnotation("Quality", "Alignment Quality based on Blosum62 scores", - new Annotation[1], - 0f, - 11f, - AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); quality.hasText = true; quality.autoCalculated = true; @@ -230,8 +253,7 @@ public class AlignViewport } consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); consensus.hasText = true; consensus.autoCalculated = true; @@ -253,10 +275,10 @@ public class AlignViewport return showSequenceFeatures; } - class ConservationThread - extends Thread + class ConservationThread extends Thread { AlignmentPanel ap; + public ConservationThread(AlignmentPanel ap) { this.ap = ap; @@ -277,8 +299,7 @@ public class AlignViewport ap.paintAlignment(false); } Thread.sleep(200); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -293,8 +314,8 @@ public class AlignViewport } Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alWidth - 1); + jalview.schemes.ResidueProperties.propHash, 3, alignment + .getSequences(), 0, alWidth - 1); cons.calculate(); cons.verdict(false, ConsPercGaps); @@ -316,7 +337,8 @@ public class AlignViewport minB = 0f; maxR = 1.0f - minR; maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and Quality + maxB = 0f - minB; // scalable range for colouring both Conservation and + // Quality float min = 0f; float max = 11f; @@ -356,29 +378,24 @@ public class AlignViewport float vprop = value - min; vprop /= max; - conservation.annotations[i] = - new Annotation(String.valueOf(c), - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); + conservation.annotations[i] = new Annotation(String.valueOf(c), + String.valueOf(value), ' ', value, new Color(minR + + (maxR * vprop), minG + (maxG * vprop), minB + + (maxB * vprop))); // Quality calc if (quality != null) { - value = ( (Double) cons.quality.elementAt(i)).floatValue(); + value = ((Double) cons.quality.elementAt(i)).floatValue(); vprop = value - qmin; vprop /= qmax; - quality.annotations[i] = new Annotation(" ", String.valueOf(value), - ' ', - value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); + quality.annotations[i] = new Annotation(" ", String + .valueOf(value), ' ', value, new Color(minR + + (maxR * vprop), minG + (maxG * vprop), minB + + (maxB * vprop))); } } - } - catch (OutOfMemoryError error) + } catch (OutOfMemoryError error) { System.out.println("Out of memory calculating conservation!!"); conservation = null; @@ -434,10 +451,10 @@ public class AlignViewport consensusThread.start(); } - class ConsensusThread - extends Thread + class ConsensusThread extends Thread { AlignmentPanel ap; + public ConsensusThread(AlignmentPanel ap) { this.ap = ap; @@ -456,8 +473,7 @@ public class AlignViewport } Thread.sleep(200); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -477,27 +493,27 @@ public class AlignViewport consensus.annotations = new Annotation[aWidth]; hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); + AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment + .getWidth(), hconsensus); for (int i = 0; i < aWidth; i++) { float value = 0; if (ignoreGapsInConsensusCalculation) { - value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)). - floatValue(); + value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) + .floatValue(); } else { - value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)). - floatValue(); + value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) + .floatValue(); } - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) + .toString(); + String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + + " "; if (maxRes.length() > 1) { @@ -505,9 +521,9 @@ public class AlignViewport maxRes = "+"; } - mouseOver += ( (int) value + "%"); + mouseOver += ((int) value + "%"); consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); + value); } if (globalColourScheme != null) @@ -515,8 +531,7 @@ public class AlignViewport globalColourScheme.setConsensus(hconsensus); } - } - catch (OutOfMemoryError error) + } catch (OutOfMemoryError error) { alignment.deleteAnnotation(consensus); @@ -536,11 +551,15 @@ public class AlignViewport } /** - * get the consensus sequence as displayed under the PID consensus annotation row. + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * * @return consensus sequence as a new sequence object */ /** - * get the consensus sequence as displayed under the PID consensus annotation row. + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * * @return consensus sequence as a new sequence object */ public SequenceI getConsensusSeq() @@ -565,9 +584,8 @@ public class AlignViewport } } SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " + - ( (ignoreGapsInConsensusCalculation) ? " without gaps" : - "")); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); return sq; } @@ -640,7 +658,8 @@ public class AlignViewport { if (res > alignment.getWidth() - 1) { - // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); + // log.System.out.println(" Corrected res from " + res + " to maximum " + + // (alignment.getWidth()-1)); res = alignment.getWidth() - 1; } if (res < 0) @@ -669,7 +688,9 @@ public class AlignViewport } java.awt.Frame nullFrame; - protected FeatureSettings featureSettings=null; + + protected FeatureSettings featureSettings = null; + public void setFont(Font f) { font = f; @@ -905,41 +926,47 @@ public class AlignViewport if (globalColourScheme != null) { globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); + ignoreGapsInConsensusCalculation); } } /** * Property change listener for changes in alignment - * - * @param listener DOCUMENT ME! + * + * @param listener + * DOCUMENT ME! */ public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) + java.beans.PropertyChangeListener listener) { changeSupport.addPropertyChangeListener(listener); } /** * DOCUMENT ME! - * - * @param listener DOCUMENT ME! + * + * @param listener + * DOCUMENT ME! */ public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) + java.beans.PropertyChangeListener listener) { changeSupport.removePropertyChangeListener(listener); } /** * Property change listener for changes in alignment - * - * @param prop DOCUMENT ME! - * @param oldvalue DOCUMENT ME! - * @param newvalue DOCUMENT ME! + * + * @param prop + * DOCUMENT ME! + * @param oldvalue + * DOCUMENT ME! + * @param newvalue + * DOCUMENT ME! */ - public void firePropertyChange(String prop, Object oldvalue, Object newvalue) + public void firePropertyChange(String prop, Object oldvalue, + Object newvalue) { changeSupport.firePropertyChange(prop, oldvalue, newvalue); } @@ -1009,7 +1036,7 @@ public class AlignViewport hiddenRepSequences.put(repSequence, sg); - //Hide all sequences except the repSequence + // Hide all sequences except the repSequence SequenceI[] seqs = new SequenceI[sSize - 1]; int index = 0; for (int i = 0; i < sSize; i++) @@ -1031,7 +1058,7 @@ public class AlignViewport public void hideAllSelectedSeqs() { - if (selectionGroup == null || selectionGroup.getSize()<1) + if (selectionGroup == null || selectionGroup.getSize() < 1) { return; } @@ -1081,12 +1108,11 @@ public class AlignViewport selectionGroup = new SequenceGroup(); selectionGroup.setEndRes(alignment.getWidth() - 1); } - Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences); + Vector tmp = alignment.getHiddenSequences().showAll( + hiddenRepSequences); for (int t = 0; t < tmp.size(); t++) { - selectionGroup.addSequence( - (SequenceI) tmp.elementAt(t), false - ); + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); } firePropertyChange("alignment", null, alignment.getSequences()); hasHiddenRows = false; @@ -1096,12 +1122,14 @@ public class AlignViewport public int adjustForHiddenSeqs(int alignmentIndex) { - return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex); + return alignment.getHiddenSequences().adjustForHiddenSeqs( + alignmentIndex); } /** - * This method returns the a new SequenceI [] with - * the selection sequence and start and end points adjusted + * This method returns the a new SequenceI [] with the selection sequence and + * start and end points adjusted + * * @return String[] */ public SequenceI[] getSelectionAsNewSequence() @@ -1121,15 +1149,15 @@ public class AlignViewport } /** - * This method returns the visible alignment as text, as - * seen on the GUI, ie if columns are hidden they will not - * be returned in the result. - * Use this for calculating trees, PCA, redundancy etc on views - * which contain hidden columns. + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * * @return String[] */ - public jalview.datamodel.CigarArray getViewAsCigars(boolean - selectedRegionOnly) + public jalview.datamodel.CigarArray getViewAsCigars( + boolean selectedRegionOnly) { CigarArray selection = null; SequenceI[] seqs = null; @@ -1140,7 +1168,8 @@ public class AlignViewport iSize = selectionGroup.getSize(); seqs = selectionGroup.getSequencesInOrder(alignment); start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor + end = selectionGroup.getEndRes(); // inclusive for start and end in + // SeqCigar constructor } else { @@ -1217,33 +1246,36 @@ public class AlignViewport } /** - * return a compact representation of the current alignment selection to - * pass to an analysis function - * @param selectedOnly boolean true to just return the selected view + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view * @return AlignmentView */ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) { // JBPNote: - // this is here because the AlignmentView constructor modifies the CigarArray + // this is here because the AlignmentView constructor modifies the + // CigarArray // object. Refactoring of Cigar and alignment view representation should // be done to remove redundancy. CigarArray aligview = getViewAsCigars(selectedOnly); if (aligview != null) { return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? - selectionGroup.getStartRes() : 0); + (selectedOnly && selectionGroup != null) ? selectionGroup + .getStartRes() : 0); } return null; } /** - * This method returns the visible alignment as text, as - * seen on the GUI, ie if columns are hidden they will not - * be returned in the result. - * Use this for calculating trees, PCA, redundancy etc on views - * which contain hidden columns. + * This method returns the visible alignment as text, as seen on the GUI, ie + * if columns are hidden they will not be returned in the result. Use this for + * calculating trees, PCA, redundancy etc on views which contain hidden + * columns. + * * @return String[] */ public String[] getViewAsString(boolean selectedRegionOnly) @@ -1379,7 +1411,7 @@ public class AlignViewport updateConservation(ap); } - //Reset endRes of groups if beyond alignment width + // Reset endRes of groups if beyond alignment width int alWidth = alignment.getWidth(); Vector groups = alignment.getGroups(); if (groups != null) @@ -1401,7 +1433,7 @@ public class AlignViewport resetAllColourSchemes(); - //AW alignment.adjustSequenceAnnotations(); + // AW alignment.adjustSequenceAnnotations(); } void resetAllColourSchemes() @@ -1411,9 +1443,8 @@ public class AlignViewport { if (cs instanceof ClustalxColourScheme) { - ( (ClustalxColourScheme) cs). - resetClustalX(alignment.getSequences(), - alignment.getWidth()); + ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(), + alignment.getWidth()); } cs.setConsensus(hconsensus); @@ -1421,9 +1452,8 @@ public class AlignViewport { Alignment al = (Alignment) alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, al + .getWidth() - 1); c.calculate(); c.verdict(false, ConsPercGaps); @@ -1437,13 +1467,15 @@ public class AlignViewport SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s); if (sg.cs != null && sg.cs instanceof ClustalxColourScheme) { - ( (ClustalxColourScheme) sg.cs).resetClustalX( - sg.getSequences(hiddenRepSequences), sg.getWidth()); + ((ClustalxColourScheme) sg.cs).resetClustalX(sg + .getSequences(hiddenRepSequences), sg.getWidth()); } sg.recalcConservation(); } } + boolean centreColumnLabels; + public boolean getCentreColumnLabels() { return centreColumnLabels; @@ -1452,16 +1484,16 @@ public class AlignViewport public void updateSequenceIdColours() { Vector groups = alignment.getGroups(); - for (int ig=0,igSize=groups.size(); ig