X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=e25818e4cd8022791d5e2b816f3afbeb3f16c106;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=f37e2bd4132ef6e8e98db453181366b140fdfbd0;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index f37e2bd..e25818e 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -1,19 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License + * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview 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 + * + * Jalview 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.viewmodel; @@ -40,7 +41,9 @@ import jalview.workers.AlignCalcManager; import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; +import java.awt.Color; import java.util.ArrayList; +import java.util.BitSet; import java.util.Hashtable; import java.util.List; import java.util.Map; @@ -209,6 +212,24 @@ public abstract class AlignmentViewport implements AlignViewportI // calculation till later or to do all calculations in thread. // via changecolour globalColourScheme = cs; + boolean recalc=false; + if (cs!=null) + { + cs.setConservationApplied(recalc = getConservationSelected()); + if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme) + { + recalc = true; + cs.setThreshold(threshold, ignoreGapsInConsensusCalculation); + } else { + cs.setThreshold(0, ignoreGapsInConsensusCalculation); + } + if (recalc) + { + cs.setConsensus(hconsensus); + cs.setConservation(hconservation); + } + cs.alignmentChanged(alignment, hiddenRepSequences); + } if (getColourAppliesToAllGroups()) { for (SequenceGroup sg : getAlignment().getGroups()) @@ -218,29 +239,13 @@ public abstract class AlignmentViewport implements AlignViewportI sg.cs = null; continue; } - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme(sg, getHiddenRepSequences()); - } - else - { - try - { - sg.cs = cs.getClass().newInstance(); - } catch (Exception ex) - { - ex.printStackTrace(); - sg.cs = cs; - } - } - + sg.cs = cs.applyTo(sg, getHiddenRepSequences()); + sg.setConsPercGaps(ConsPercGaps); if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(getHiddenRepSequences()), 0, - sg.getWidth())); + recalc=true; } else { @@ -249,20 +254,19 @@ public abstract class AlignmentViewport implements AlignViewportI if (getConservationSelected()) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(getHiddenRepSequences()), 0, - getAlignment().getWidth() - 1); - c.calculate(); - c.verdict(false, getConsPercGaps()); - sg.cs.setConservation(c); + sg.cs.setConservationApplied(true); + recalc=true; } else { sg.cs.setConservation(null); - sg.cs.setThreshold(0, getIgnoreGapsConsensus()); + // sg.cs.setThreshold(0, getIgnoreGapsConsensus()); + } + if (recalc) { + sg.recalcConservation(); + } else { + sg.cs.alignmentChanged(sg, hiddenRepSequences); } - } } @@ -296,7 +300,13 @@ public abstract class AlignmentViewport implements AlignViewportI * view */ protected Hashtable[] hStrucConsensus = null; - + + protected Conservation hconservation = null; + @Override + public void setConservation(Conservation cons) + { + hconservation = cons; + } /** * percentage gaps allowed in a column before all amino acid properties should * be considered unconserved @@ -402,7 +412,8 @@ public abstract class AlignmentViewport implements AlignViewportI if (autoCalculateStrucConsensus && strucConsensus == null && alignment.isNucleotide() && alignment.hasRNAStructure()) { - + // secondary structure has been added - so init the consensus line + initRNAStructure(); } // see note in mantis : issue number 8585 @@ -593,6 +604,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @return null or the currently selected sequence region */ + @Override public SequenceGroup getSelectionGroup() { return selectionGroup; @@ -605,6 +617,7 @@ public abstract class AlignmentViewport implements AlignViewportI * - group holding references to sequences in this alignment view * */ + @Override public void setSelectionGroup(SequenceGroup sg) { selectionGroup = sg; @@ -780,6 +793,8 @@ public abstract class AlignmentViewport implements AlignViewportI protected boolean showConsensus = true; + Hashtable sequenceColours; + /** * Property change listener for changes in alignment * @@ -1053,6 +1068,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @return array of references to sequence objects */ + @Override public SequenceI[] getSequenceSelection() { SequenceI[] sequences = null; @@ -1075,6 +1091,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @return String[] */ + @Override public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { @@ -1091,6 +1108,7 @@ public abstract class AlignmentViewport implements AlignViewportI * boolean true to just return the selected view * @return AlignmentView */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) { @@ -1109,6 +1127,7 @@ public abstract class AlignmentViewport implements AlignViewportI * is true) * @return AlignmentView */ + @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly, boolean markGroups) { @@ -1124,6 +1143,7 @@ public abstract class AlignmentViewport implements AlignViewportI * * @return String[] */ + @Override public String[] getViewAsString(boolean selectedRegionOnly) { String[] selection = null; @@ -1287,7 +1307,7 @@ public abstract class AlignmentViewport implements AlignViewportI ColourSchemeI cs = globalColourScheme; if (cs != null) { - cs.alignmentChanged(alignment, null); + cs.alignmentChanged(alignment, hiddenRepSequences); cs.setConsensus(hconsensus); if (cs.conservationApplied()) @@ -1318,62 +1338,80 @@ public abstract class AlignmentViewport implements AlignViewportI { if (!alignment.isNucleotide()) { - if (showConservation) - { - if (conservation == null) - { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " - + getConsPercGaps() + "% gaps", - new Annotation[1], 0f, 11f, - AlignmentAnnotation.BAR_GRAPH); - conservation.hasText = true; - conservation.autoCalculated = true; - alignment.addAnnotation(conservation); - } - } - if (showQuality) - { - if (quality == null) - { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], 0f, 11f, - AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - quality.autoCalculated = true; - alignment.addAnnotation(quality); - } - } + initConservation(); + initQuality(); } else { - if (alignment.hasRNAStructure()) - { - strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", - new Annotation[1], 0f, 100f, - AlignmentAnnotation.BAR_GRAPH); - strucConsensus.hasText = true; - strucConsensus.autoCalculated = true; - } + initRNAStructure(); } + initConsensus(); + } + } - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; + private void initConsensus() + { - if (showConsensus) + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + consensus.autoCalculated = true; + + if (showConsensus) + { + alignment.addAnnotation(consensus); + } + } + + private void initConservation() + { + if (showConservation) + { + if (conservation == null) { - alignment.addAnnotation(consensus); - if (strucConsensus != null) - { - alignment.addAnnotation(strucConsensus); - } + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + + getConsPercGaps() + "% gaps", + new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + conservation.autoCalculated = true; + alignment.addAnnotation(conservation); + } + } + } + private void initQuality() + { + if (showQuality) + { + if (quality == null) + { + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; + alignment.addAnnotation(quality); } } } + private void initRNAStructure() + { + if (alignment.hasRNAStructure() && strucConsensus==null) + { + strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + strucConsensus.hasText = true; + strucConsensus.autoCalculated = true; + if (showConsensus) + { + alignment.addAnnotation(strucConsensus); + } + } + } /* * (non-Javadoc) * @@ -1387,7 +1425,7 @@ public abstract class AlignmentViewport implements AlignViewportI int charHeight = getCharHeight(); if (aa != null) { - boolean graphgrp[] = null; + BitSet graphgrp = new BitSet(); for (int i = 0; i < aa.length; i++) { if (aa[i] == null) @@ -1401,17 +1439,13 @@ public abstract class AlignmentViewport implements AlignViewportI } if (aa[i].graphGroup > -1) { - if (graphgrp == null) - { - graphgrp = new boolean[aa.length]; - } - if (graphgrp[aa[i].graphGroup]) + if (graphgrp.get(aa[i].graphGroup)) { continue; } else { - graphgrp[aa[i].graphGroup] = true; + graphgrp.set(aa[i].graphGroup); } } aa[i].height = 0; @@ -1478,8 +1512,7 @@ public abstract class AlignmentViewport implements AlignViewportI if (aan[an].autoCalculated && aan[an].groupRef != null) { oldrfs.add(aan[an].groupRef); - alignment.deleteAnnotation(aan[an]); - aan[an] = null; + alignment.deleteAnnotation(aan[an],false); } } } @@ -1516,4 +1549,60 @@ public abstract class AlignmentViewport implements AlignViewportI oldrfs.clear(); } + @Override + public Color getSequenceColour(SequenceI seq) + { + Color sqc=Color.white; + if (sequenceColours != null) + { + sqc = (Color) sequenceColours.get(seq); + if (sqc == null) { + sqc = Color.white; + } + } + return sqc; + } + + @Override + public void setSequenceColour(SequenceI seq, Color col) + { + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + + if (col == null) + { + sequenceColours.remove(seq); + } + else + { + sequenceColours.put(seq, col); + } + } + + @Override + public void updateSequenceIdColours() + { + if (sequenceColours == null) + { + sequenceColours = new Hashtable(); + } + for (SequenceGroup sg : alignment.getGroups()) + { + if (sg.idColour != null) + { + for (SequenceI s : sg.getSequences(getHiddenRepSequences())) + { + sequenceColours.put(s, sg.idColour); + } + } + } + } + + @Override + public void clearSequenceColours() + { + sequenceColours = null; + }; }