From eeaf210a324ea2677c8267531ffb78e1c19fada1 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 24 Jul 2009 15:23:01 +0000 Subject: [PATCH] refactored conservation thread, added showgroupannotation flags --- src/jalview/gui/AlignViewport.java | 217 ++++++++---------------------------- 1 file changed, 44 insertions(+), 173 deletions(-) diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 8c23e4d..70ca6f2 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -142,7 +142,9 @@ public class AlignViewport implements SelectionSource AlignmentAnnotation conservation; AlignmentAnnotation quality; - + AlignmentAnnotation[] groupConsensus; + AlignmentAnnotation[] groupConservation; + boolean autoCalculateConsensus = true; /** DOCUMENT ME!! */ @@ -395,146 +397,6 @@ public class AlignViewport implements SelectionSource return showSequenceFeatures; } - class ConservationThread extends Thread - { - AlignmentPanel ap; - - public ConservationThread(AlignmentPanel ap) - { - this.ap = ap; - } - - public void run() - { - try - { - updatingConservation = true; - - while (UPDATING_CONSERVATION) - { - try - { - if (ap != null) - { - ap.paintAlignment(false); - } - Thread.sleep(200); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - UPDATING_CONSERVATION = true; - - int alWidth = alignment.getWidth(); - if (alWidth < 0) - { - return; - } - - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, alignment - .getSequences(), 0, alWidth - 1); - - cons.calculate(); - cons.verdict(false, ConsPercGaps); - - if (quality != null) - { - cons.findQuality(); - } - - char[] sequence = cons.getConsSequence().getSequence(); - float minR; - float minG; - float minB; - float maxR; - float maxG; - float maxB; - minR = 0.3f; - minG = 0.0f; - minB = 0f; - maxR = 1.0f - minR; - maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and - // Quality - - float min = 0f; - float max = 11f; - float qmin = 0f; - float qmax = 0f; - - char c; - - conservation.annotations = new Annotation[alWidth]; - - if (quality != null) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - quality.annotations = new Annotation[alWidth]; - qmin = cons.qualityRange[0].floatValue(); - qmax = cons.qualityRange[1].floatValue(); - } - - for (int i = 0; i < alWidth; i++) - { - float value = 0; - - c = sequence[i]; - - if (Character.isDigit(c)) - { - value = (int) (c - '0'); - } - else if (c == '*') - { - value = 11; - } - else if (c == '+') - { - value = 10; - } - - 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))); - - // Quality calc - if (quality != null) - { - value = ((Double) cons.quality.get(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))); - } - } - } catch (OutOfMemoryError error) - { - new OOMWarning("calculating conservation", error); - - conservation = null; - quality = null; - - } - - UPDATING_CONSERVATION = false; - updatingConservation = false; - - if (ap != null) - { - ap.paintAlignment(true); - } - - } - } - ConservationThread conservationThread; ConsensusThread consensusThread; @@ -570,7 +432,7 @@ public class AlignViewport implements SelectionSource return; } - conservationThread = new ConservationThread(ap); + conservationThread = new ConservationThread(this, ap); conservationThread.start(); } @@ -635,37 +497,8 @@ public class AlignViewport implements SelectionSource hconsensus = new Hashtable[aWidth]; 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(); - } - else - { - value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) - .floatValue(); - } - - String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE) - .toString(); - String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) - + " "; - - if (maxRes.length() > 1) - { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; - } - - mouseOver += ((int) value + "%"); - consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', - value); - } - + AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation); + if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -2236,4 +2069,42 @@ public class AlignViewport implements SelectionSource public void setSortByTree(boolean sort) { sortByTree = sort; } + /** + * should conservation rows be shown for groups + */ + boolean showGroupConservation = false; + /** + * should consensus rows be shown for groups + */ + boolean showGroupConsensus = false; + + /** + * @return the showGroupConservation + */ + public boolean isShowGroupConservation() + { + return showGroupConservation; + } + /** + * @param showGroupConservation the showGroupConservation to set + */ + public void setShowGroupConservation(boolean showGroupConservation) + { + this.showGroupConservation = showGroupConservation; + } + /** + * @return the showGroupConsensus + */ + public boolean isShowGroupConsensus() + { + return showGroupConsensus; + } + /** + * @param showGroupConsensus the showGroupConsensus to set + */ + public void setShowGroupConsensus(boolean showGroupConsensus) + { + this.showGroupConsensus = showGroupConsensus; + } + } -- 1.7.10.2