X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7a01b274520cd95d72c9b0f51bf84d77555bb332;hb=59d682209891099d46b960509907c79e3fb276fe;hp=8f615aa55480e4eda1d6155f2e371d13e0b0dcd7;hpb=746d44733521ab266aea00b724175a6ade377bcd;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 8f615aa..7a01b27 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/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 @@ -35,29 +35,33 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; - -import jalview.analysis.*; -import jalview.api.AlignCalcManagerI; +import jalview.analysis.NJTree; import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.api.OOMHandlerI; - -import jalview.bin.*; - -import jalview.datamodel.*; - -import jalview.schemes.*; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.viewmodel.AlignmentViewport; -import jalview.workers.AlignCalcManager; -import jalview.workers.ConsensusThread; -import jalview.workers.ConservationThread; -import jalview.workers.StrucConsensusThread; +import jalview.ws.params.AutoCalcSetting; + +import java.awt.Color; +import java.awt.Container; +import java.awt.Font; +import java.awt.Rectangle; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.Stack; +import java.util.Vector; /** * DOCUMENT ME! @@ -65,10 +69,9 @@ import jalview.workers.StrucConsensusThread; * @author $author$ * @version $Revision: 1.141 $ */ -public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI +public class AlignViewport extends AlignmentViewport implements + SelectionSource, VamsasSource, AlignViewportI { - private static final int RIGHT_JUSTIFY = 1; - int startRes; int endRes; @@ -93,12 +96,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, boolean showAnnotation = true; - boolean colourAppliesToAllGroups = true; - - boolean conservationColourSelected = false; - - boolean abovePIDThreshold = false; - int charHeight; int charWidth; @@ -111,10 +108,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, boolean seqNameItalics; - int threshold; - - int increment; - NJTree currentTree = null; boolean scaleAboveWrapped = false; @@ -328,17 +321,18 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, { if (!alignment.isNucleotide()) { - showConservation=Cache.getDefault("SHOW_CONSERVATION", true); - showQuality=Cache.getDefault("SHOW_QUALITY", true); + showConservation = Cache.getDefault("SHOW_CONSERVATION", true); + showQuality = Cache.getDefault("SHOW_QUALITY", true); showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", false); - } + } showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true); showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false); - normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false); + normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", + false); showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); - showConsensus=Cache.getDefault("SHOW_IDENTITY", true); + showConsensus = Cache.getDefault("SHOW_IDENTITY", true); consensus = new AlignmentAnnotation("Consensus", "PID", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); consensus.hasText = true; @@ -437,50 +431,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, return sq; } - - /** - * GUI state - * - * @return true if conservation based shading is enabled - */ - public boolean getConservationSelected() - { - return conservationColourSelected; - } - - /** - * GUI state - * - * @param b - * enable conservation based shading - */ - public void setConservationSelected(boolean b) - { - conservationColourSelected = b; - } - - /** - * GUI state - * - * @return true if percent identity threshold is applied to shading - */ - public boolean getAbovePIDThreshold() - { - return abovePIDThreshold; - } - - /** - * GUI state - * - * - * @param b - * indicate if percent identity threshold is applied to shading - */ - public void setAbovePIDThreshold(boolean b) - { - abovePIDThreshold = b; - } - /** * DOCUMENT ME! * @@ -702,7 +652,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, Desktop.instance).removeMappings(alignment.getCodonFrames()); } this.alignment = align; - if (alignment!=null && alignment.getCodonFrames() != null) + if (alignment != null && alignment.getCodonFrames() != null) { StructureSelectionManager.getStructureSelectionManager( Desktop.instance).addMappings(alignment.getCodonFrames()); @@ -831,48 +781,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, /** * DOCUMENT ME! * - * @param thresh - * DOCUMENT ME! - */ - public void setThreshold(int thresh) - { - threshold = thresh; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getThreshold() - { - return threshold; - } - - /** - * DOCUMENT ME! - * - * @param inc - * DOCUMENT ME! - */ - public void setIncrement(int inc) - { - increment = inc; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getIncrement() - { - return increment; - } - - /** - * DOCUMENT ME! - * * @return DOCUMENT ME! */ public ColumnSelection getColumnSelection() @@ -904,27 +812,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, /** * DOCUMENT ME! * - * @param b - * DOCUMENT ME! - */ - public void setColourAppliesToAllGroups(boolean b) - { - colourAppliesToAllGroups = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourAppliesToAllGroups() - { - return colourAppliesToAllGroups; - } - - /** - * DOCUMENT ME! - * * @return DOCUMENT ME! */ public boolean getShowJVSuffix() @@ -1027,7 +914,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, scaleRightWrapped = b; } - public void setDataset(boolean b) { isDataset = b; @@ -1038,8 +924,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, return isDataset; } - - public boolean getShowHiddenMarkers() { return showHiddenMarkers; @@ -1111,6 +995,7 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, */ public long[] getUndoRedoHash() { + // TODO: JAL-1126 if (historyList == null || redoList == null) return new long[] { -1, -1 }; @@ -1161,20 +1046,17 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, public void updateSequenceIdColours() { - Vector groups = alignment.getGroups(); if (sequenceColours == null) { sequenceColours = new Hashtable(); } - 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())) { - sequenceColours.put(sqs.elementAt(s), sg.idColour); + sequenceColours.put(s, sg.idColour); } } } @@ -1390,7 +1272,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, return seqvectors.toArray(new SequenceI[seqvectors.size()][]); } - public boolean isNormaliseSequenceLogo() { return normaliseSequenceLogo; @@ -1401,13 +1282,32 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource, normaliseSequenceLogo = state; } - /** * - * @return true if alignment characters should be displayed + * @return true if alignment characters should be displayed */ public boolean isValidCharWidth() { return validCharWidth; } + + private Hashtable calcIdParams = new Hashtable(); + + public AutoCalcSetting getCalcIdSettingsFor(String calcId) + { + return calcIdParams.get(calcId); + } + + public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, + boolean needsUpdate) + { + calcIdParams.put(calcId, settings); + // TODO: create a restart list to trigger any calculations that need to be + // restarted after load + // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass()) + if (needsUpdate) + { + Cache.log.debug("trigger update for " + calcId); + } + } }