X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=87566c609716897040c77fcb68304b7e14cd11ab;hb=4367b86b1364ac33a25024d7564ba57310b93f21;hp=804b590867c5741efe414fcb34b8c6ac84faa49a;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 804b590..87566c6 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -25,8 +25,10 @@ import jalview.analysis.*; import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.VamsasSource; -public class AlignViewport +public class AlignViewport implements SelectionSource, VamsasSource { int startRes; @@ -129,7 +131,7 @@ public class AlignViewport boolean ignoreGapsInConsensusCalculation = false; - jalview.bin.JalviewLite applet; + public jalview.bin.JalviewLite applet; Hashtable sequenceColours; @@ -256,7 +258,24 @@ public class AlignViewport { sortByTree = Boolean.valueOf(param).booleanValue(); } - + param = applet.getParameter("automaticScrolling"); + if (param!=null) { + followHighlight = Boolean.valueOf(param).booleanValue(); + followSelection = followHighlight; + } + if ((param=applet.getParameter("showSequenceLogo"))!=null) { + showSequenceLogo=Boolean.valueOf(param).booleanValue(); + } + if ((param=applet.getParameter("showGroupConsensus"))!=null) { + showGroupConsensus=Boolean.valueOf(param).booleanValue(); + } + if ((param=applet.getParameter("showGroupConservation"))!=null) { + showGroupConservation=Boolean.valueOf(param).booleanValue(); + } + if ((param=applet.getParameter("showConsensusHistogram"))!=null) { + showConsensusHistogram=Boolean.valueOf(param).booleanValue(); + } + } if (applet != null) @@ -371,9 +390,11 @@ public class AlignViewport UPDATING_CONSERVATION = true; - int alWidth = alignment.getWidth(); + int alWidth = (alignment==null) ? -1 : alignment.getWidth(); if (alWidth < 0) { + updatingConservation = false; + UPDATING_CONSERVATION = false; return; } @@ -548,9 +569,11 @@ public class AlignViewport try { - int aWidth = alignment.getWidth(); + int aWidth = alignment==null ? -1 : alignment.getWidth(); if (aWidth < 0) { + UPDATING_CONSENSUS = false; + updatingConsensus = false; return; } @@ -561,10 +584,11 @@ 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); @@ -587,6 +611,28 @@ 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); + } + } } /** @@ -599,6 +645,10 @@ public class AlignViewport { if (consensus == null) { + updateConsensus(null); + } + if (consensus == null) + { return null; } StringBuffer seqs = new StringBuffer(); @@ -1118,7 +1168,31 @@ 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); @@ -1152,6 +1226,7 @@ public class AlignViewport firePropertyChange("alignment", null, alignment.getSequences()); hasHiddenRows = false; hiddenRepSequences = null; + sendSelection(); } } @@ -1214,90 +1289,7 @@ public class AlignViewport public jalview.datamodel.CigarArray getViewAsCigars( boolean selectedRegionOnly) { - CigarArray selection = null; - SequenceI[] seqs = null; - int i, iSize; - int start = 0, end = 0; - if (selectedRegionOnly && selectionGroup != null) - { - iSize = selectionGroup.getSize(); - seqs = selectionGroup.getSequencesInOrder(alignment); - start = selectionGroup.getStartRes(); - end = selectionGroup.getEndRes(); // inclusive for start and end in - // SeqCigar constructor - } - else - { - iSize = alignment.getHeight(); - seqs = alignment.getSequencesArray(); - end = alignment.getWidth() - 1; - } - SeqCigar[] selseqs = new SeqCigar[iSize]; - for (i = 0; i < iSize; i++) - { - selseqs[i] = new SeqCigar(seqs[i], start, end); - } - selection = new CigarArray(selseqs); - // now construct the CigarArray operations - if (hasHiddenColumns) - { - Vector regions = colSel.getHiddenColumns(); - int[] region; - int hideStart, hideEnd; - int last = start; - for (int j = 0; last < end & j < regions.size(); j++) - { - region = (int[]) regions.elementAt(j); - hideStart = region[0]; - hideEnd = region[1]; - // edit hidden regions to selection range - if (hideStart < last) - { - if (hideEnd > last) - { - hideStart = last; - } - else - { - continue; - } - } - - if (hideStart > end) - { - break; - } - - if (hideEnd > end) - { - hideEnd = end; - } - - if (hideStart > hideEnd) - { - break; - } - /** - * form operations... - */ - if (last < hideStart) - { - selection.addOperation(CigarArray.M, hideStart - last); - } - selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart); - last = hideEnd + 1; - } - // Final match if necessary. - if (last < end) - { - selection.addOperation(CigarArray.M, end - last + 1); - } - } - else - { - selection.addOperation(CigarArray.M, end - start + 1); - } - return selection; + return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null)); } /** @@ -1309,22 +1301,24 @@ public class AlignViewport * @return AlignmentView */ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) + { + return getAlignmentView(selectedOnly, false); + } + + /** + * return a compact representation of the current alignment selection to pass + * to an analysis function + * + * @param selectedOnly + * boolean true to just return the selected view + * @param markGroups + * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true) + * @return AlignmentView + */ + public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups) { - // JBPNote: - // this is here because the AlignmentView constructor modifies the - // CigarArray - // object. Refactoring of Cigar and alignment view representation should - // be done to remove redundancy. - CigarArray aligview = getViewAsCigars(selectedOnly); - if (aligview != null) - { - return new AlignmentView(aligview, - (selectedOnly && selectionGroup != null) ? selectionGroup - .getStartRes() : 0); - } - return null; + return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups); } - /** * This method returns the visible alignment as text, as seen on the GUI, ie * if columns are hidden they will not be returned in the result. Use this for @@ -1455,6 +1449,20 @@ 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) { @@ -1560,6 +1568,63 @@ public class AlignViewport 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().sendSelection( + new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), this); + } + + + + /** * show non-conserved residues only */ @@ -1588,27 +1653,17 @@ 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; @@ -1627,24 +1682,64 @@ 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; } /** @@ -1689,5 +1784,4 @@ public class AlignViewport } } } - }