X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ff8f7df33959c561cc8eefe9cdd119a15e87edab;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=62c313fe5e3623c1b7ac8f306b3da4ab7917c7cd;hpb=3b37db6ed63140990a6cf5a7d36875b94e90a5df;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java old mode 100755 new mode 100644 index 62c313f..ff8f7df --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -25,8 +25,11 @@ import jalview.analysis.*; import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.structure.VamsasSource; -public class AlignViewport +public class AlignViewport implements SelectionSource, VamsasSource { int startRes; @@ -129,7 +132,7 @@ public class AlignViewport boolean ignoreGapsInConsensusCalculation = false; - jalview.bin.JalviewLite applet; + public jalview.bin.JalviewLite applet; Hashtable sequenceColours; @@ -142,6 +145,13 @@ public class AlignViewport String sequenceSetID; Hashtable hiddenRepSequences; + + public void finalize() { + applet=null; + quality=null; + alignment=null; + colSel=null; + } public AlignViewport(AlignmentI al, JalviewLite applet) { @@ -207,43 +217,19 @@ public class AlignViewport if (applet != null) { - String param = applet.getParameter("showFullId"); - if (param != null) - { - showJVSuffix = Boolean.valueOf(param).booleanValue(); - } + showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix); - param = applet.getParameter("showAnnotation"); - if (param != null) - { - showAnnotation = Boolean.valueOf(param).booleanValue(); - } + showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation); + + showConservation = applet.getDefaultParameter("showConservation", showConservation); + + showQuality = applet.getDefaultParameter("showQuality", showQuality); - param = applet.getParameter("showConservation"); - if (param != null) - { - showConservation = Boolean.valueOf(param).booleanValue(); - } + showConsensus = applet.getDefaultParameter("showConsensus", showConsensus); - param = applet.getParameter("showQuality"); - if (param != null) - { - showQuality = Boolean.valueOf(param).booleanValue(); - } + showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved); - param = applet.getParameter("showConsensus"); - if (param != null) - { - showConsensus = Boolean.valueOf(param).booleanValue(); - } - - param = applet.getParameter("showUnconserved"); - if (param != null) - { - this.showUnconserved = Boolean.valueOf(param).booleanValue(); - } - - param = applet.getParameter("upperCase"); + String param = applet.getParameter("upperCase"); if (param != null) { if (param.equalsIgnoreCase("bold")) @@ -251,12 +237,19 @@ public class AlignViewport upperCasebold = true; } } - param = applet.getParameter("sortByTree"); - if (param != null) - { - sortByTree = Boolean.valueOf(param).booleanValue(); - } - + sortByTree = applet.getDefaultParameter("sortByTree", sortByTree); + + followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight); + followSelection = followHighlight; + + showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo); + + showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus); + + showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation); + + showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram); + } if (applet != null) @@ -565,10 +558,11 @@ public class AlignViewport AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment.getWidth(), hconsensus, true); // always calculate the // full profile - AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth, - ignoreGapsInConsensusCalculation, - includeAllConsensusSymbols); - + updateAnnotation(true); + //AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth, + // ignoreGapsInConsensusCalculation, + // true); + if (globalColourScheme != null) { globalColourScheme.setConsensus(hconsensus); @@ -591,6 +585,28 @@ public class AlignViewport ap.paintAlignment(true); } } + + /** + * update the consensus annotation from the sequence profile data using + * current visualization settings. + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + protected void updateAnnotation(boolean immediate) + { + // TODO: make calls thread-safe, so if another thread calls this method, + // it will either return or wait until one calculation is finished. + if (immediate + || (!updatingConsensus && consensus != null && hconsensus != null)) + { + AAFrequency.completeConsensus(consensus, hconsensus, 0, + hconsensus.length, ignoreGapsInConsensusCalculation, + showSequenceLogo); + } + } } /** @@ -603,6 +619,10 @@ public class AlignViewport { if (consensus == null) { + updateConsensus(null); + } + if (consensus == null) + { return null; } StringBuffer seqs = new StringBuffer(); @@ -1122,7 +1142,31 @@ public class AlignViewport firePropertyChange("alignment", null, alignment.getSequences()); } } + public void showSequence(int index) + { + Vector tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); + if (tmp.size() > 0) + { + if (selectionGroup == null) + { + selectionGroup = new SequenceGroup(); + selectionGroup.setEndRes(alignment.getWidth() - 1); + } + + for (int t = 0; t < tmp.size(); t++) + { + selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); + } + firePropertyChange("alignment", null, alignment.getSequences()); + sendSelection(); + } + if (alignment.getHiddenSequences().getSize() < 1) + { + hasHiddenRows = false; + } + } public void showColumn(int col) { colSel.revealHiddenColumns(col); @@ -1156,6 +1200,7 @@ public class AlignViewport firePropertyChange("alignment", null, alignment.getSequences()); hasHiddenRows = false; hiddenRepSequences = null; + sendSelection(); } } @@ -1378,6 +1423,20 @@ public class AlignViewport return sequenceSetID; } + /** + * unique viewId for synchronizing state (e.g. with stored Jalview Project) + * + */ + private String viewId = null; + + public String getViewId() + { + if (viewId == null) + { + viewId = this.getSequenceSetId() + "." + this.hashCode() + ""; + } + return viewId; + } public void alignmentChanged(AlignmentPanel ap) { @@ -1476,13 +1535,70 @@ public class AlignViewport } } - public boolean followHighlight = false; + public boolean followHighlight = true; public boolean getFollowHighlight() { return followHighlight; } + public boolean followSelection = true; + + /** + * @return true if view selection should always follow the selections + * broadcast by other selection sources + */ + public boolean getFollowSelection() + { + return followSelection; + } + + private long sgrouphash = -1, colselhash = -1; + + /** + * checks current SelectionGroup against record of last hash value, and + * updates record. + * + * @return true if SelectionGroup changed since last call + */ + boolean isSelectionGroupChanged() + { + int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode(); + if (hc != sgrouphash) + { + sgrouphash = hc; + return true; + } + return false; + } + + /** + * checks current colsel against record of last hash value, and updates + * record. + * + * @return true if colsel changed since last call + */ + boolean isColSelChanged() + { + int hc = (colSel == null) ? -1 : colSel.hashCode(); + if (hc != colselhash) + { + colselhash = hc; + return true; + } + return false; + } + public void sendSelection() + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(applet).sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + + + /** * show non-conserved residues only */ @@ -1511,27 +1627,17 @@ public class AlignViewport } /** - * consensus annotation includes all percentage for all symbols in column - * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1 - * compatible) - */ - private boolean includeAllConsensusSymbols = false; - - /** - * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug - * 62446) + * should conservation rows be shown for groups */ boolean showGroupConservation = false; /** - * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug - * 62446) + * should consensus rows be shown for groups */ boolean showGroupConsensus = false; /** - * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE - * (bug #60064 logo rendering is not AWT 1.1 compatible) + * should consensus profile be rendered by default */ public boolean showSequenceLogo = false; @@ -1550,24 +1656,64 @@ public class AlignViewport /** * @param showSequenceLogo - * the new value public void setShowSequenceLogo(boolean - * showSequenceLogo) { this.showSequenceLogo = showSequenceLogo; } + * the new value */ + public void setShowSequenceLogo(boolean showSequenceLogo) + { + if (showSequenceLogo != this.showSequenceLogo) + { + // TODO: decouple settings setting from calculation when refactoring + // annotation update method from alignframe to viewport + this.showSequenceLogo = showSequenceLogo; + if (consensusThread != null) + { + consensusThread.updateAnnotation(); + } + } + this.showSequenceLogo = showSequenceLogo; + } + /** - * @param showGroupConsensus - * the showGroupConsensus to set + * @param showConsensusHistogram + * the showConsensusHistogram to set */ - public void setShowGroupConsensus(boolean showGroupConsensus) + public void setShowConsensusHistogram(boolean showConsensusHistogram) { - this.showGroupConsensus = showGroupConsensus; + this.showConsensusHistogram = showConsensusHistogram; } /** - * @return the includeAllConsensusSymbols + * @return the showGroupConservation */ - public boolean isIncludeAllConsensusSymbols() + public boolean isShowGroupConservation() { - return false; + 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; } /** @@ -1612,5 +1758,4 @@ public class AlignViewport } } } - }