X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=cc04b581000251b40d94935b01f29c997dcdd1a7;hb=2bd43f464e725844b02a106c2d2f187c2c3655a6;hp=ab9a25d66ae1886f5e07c98391ae279c4cf36dd9;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index ab9a25d..cc04b58 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * 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) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * 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 * 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 @@ -22,7 +22,6 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; -import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; import jalview.bin.*; import jalview.datamodel.*; @@ -30,10 +29,9 @@ import jalview.schemes.*; import jalview.structure.SelectionSource; import jalview.structure.VamsasSource; import jalview.viewmodel.AlignmentViewport; -import jalview.workers.ConservationThread; -import jalview.workers.ConsensusThread; -public class AlignViewport extends AlignmentViewport implements AlignViewportI, SelectionSource, VamsasSource +public class AlignViewport extends AlignmentViewport implements + AlignViewportI, SelectionSource, VamsasSource { int startRes; @@ -61,20 +59,8 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, boolean showAnnotation = true; - boolean showConservation = true; - - boolean showQuality = true; - - boolean showConsensus = true; - boolean upperCasebold = false; - boolean colourAppliesToAllGroups = true; - - boolean conservationColourSelected = false; - - boolean abovePIDThreshold = false; - int charHeight; int charWidth; @@ -101,7 +87,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, // currently visible, in the correct order or rendering public Hashtable featuresDisplayed; - boolean showHiddenMarkers = true; public jalview.bin.JalviewLite applet; @@ -113,12 +98,13 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, Stack historyList = new Stack(); Stack redoList = new Stack(); - - public void finalize() { - applet=null; - quality=null; - alignment=null; - colSel=null; + + public void finalize() + { + applet = null; + quality = null; + alignment = null; + colSel = null; } public AlignViewport(AlignmentI al, JalviewLite applet) @@ -190,15 +176,19 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, { showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix); - showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation); - - showConservation = applet.getDefaultParameter("showConservation", showConservation); - + showAnnotation = applet.getDefaultParameter("showAnnotation", + showAnnotation); + + showConservation = applet.getDefaultParameter("showConservation", + showConservation); + showQuality = applet.getDefaultParameter("showQuality", showQuality); - showConsensus = applet.getDefaultParameter("showConsensus", showConsensus); + showConsensus = applet.getDefaultParameter("showConsensus", + showConsensus); - showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved); + showUnconserved = applet.getDefaultParameter("showUnconserved", + showUnconserved); String param = applet.getParameter("upperCase"); if (param != null) @@ -210,19 +200,26 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, } sortByTree = applet.getDefaultParameter("sortByTree", sortByTree); - followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight); + followHighlight = applet.getDefaultParameter("automaticScrolling", + followHighlight); followSelection = followHighlight; - showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo); + showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", + showSequenceLogo); + + normaliseSequenceLogo = applet.getDefaultParameter( + "normaliseSequenceLogo", applet.getDefaultParameter( + "normaliseLogo", normaliseSequenceLogo)); + + showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", + showGroupConsensus); + + showGroupConservation = applet.getDefaultParameter( + "showGroupConservation", showGroupConservation); - normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo); + showConsensusHistogram = applet.getDefaultParameter( + "showConsensusHistogram", showConsensusHistogram); - showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus); - - showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation); - - showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram); - } if (applet != null) @@ -254,44 +251,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, .getParameter("userDefinedColour")); } } - if (hconsensus == null) - { - if (!alignment.isNucleotide()) - { - 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; - - if (showConservation) - { - alignment.addAnnotation(conservation); - } - - if (showQuality) - { - 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); - } - } - - consensus = new AlignmentAnnotation("Consensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); - consensus.hasText = true; - consensus.autoCalculated = true; - - if (showConsensus) - { - alignment.addAnnotation(consensus); - } - } + initAutoAnnotation(); } @@ -305,7 +265,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, return showSequenceFeatures; } - /** * get the consensus sequence as displayed under the PID consensus annotation * row. @@ -343,26 +302,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, return sq; } - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - public int getStartRes() { return startRes; @@ -581,16 +520,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, return currentTree; } - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } - - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } - public boolean getShowJVSuffix() { return showJVSuffix; @@ -653,10 +582,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, } } - - - - public boolean getShowHiddenMarkers() { return showHiddenMarkers; @@ -705,16 +630,14 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, public void updateSequenceIdColours() { - Vector groups = alignment.getGroups(); - for (int ig = 0, igSize = groups.size(); ig < igSize; ig++) + + for (SequenceGroup sg : alignment.getGroups()) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(ig); if (sg.idColour != null) { - Vector sqs = sg.getSequences(getHiddenRepSequences()); - for (int s = 0, sSize = sqs.size(); s < sSize; s++) + for (SequenceI s : sg.getSequences(getHiddenRepSequences())) { - this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour); + this.setSequenceColour(s, sg.idColour); } } } @@ -737,6 +660,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, { return followSelection; } + public void sendSelection() { jalview.structure.StructureSelectionManager @@ -745,9 +669,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, new ColumnSelection(getColumnSelection()), this); } - - - /** * synthesize a column selection if none exists so it covers the given * selection group. if wholewidth is false, no column selection is made if the @@ -786,7 +707,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, { return hasHiddenColumns; } - + public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; @@ -799,7 +720,7 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI, /** * - * @return true if alignment characters should be displayed + * @return true if alignment characters should be displayed */ public boolean isValidCharWidth() {