X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a15e9a67b0300ebf547796632e7d68df93fb93bc;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d8ade26158f0cb9344e5e28846e4f1f18f813fba;hpb=0089e3442ccafc1073eff6055ef458745aabce18;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index d8ade26..a15e9a6 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,17 +20,6 @@ */ package jalview.viewmodel; -import java.awt.Color; -import java.util.ArrayDeque; -import java.util.ArrayList; -import java.util.BitSet; -import java.util.Deque; -import java.util.HashMap; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; -import java.util.Set; - import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; import jalview.api.AlignCalcManagerI; @@ -67,6 +56,17 @@ import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; import jalview.workers.StrucConsensusThread; +import java.awt.Color; +import java.util.ArrayDeque; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Deque; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.Set; + /** * base class holding visualization and analysis attributes and common logic for * an active alignment view displayed in the GUI @@ -75,7 +75,7 @@ import jalview.workers.StrucConsensusThread; * */ public abstract class AlignmentViewport implements AlignViewportI, - ViewStyleI, CommandListener, VamsasSource + CommandListener, VamsasSource { protected ViewStyleI viewStyle = new ViewStyle(); @@ -506,15 +506,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } /** - * @param selected - * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean) - */ - public void setShowSeqFeaturesHeight(boolean selected) - { - viewStyle.setShowSeqFeaturesHeight(selected); - } - - /** * alignment displayed in the viewport. Please use get/setter */ protected AlignmentI alignment; @@ -549,7 +540,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return isDataset; } - private Map hiddenRepSequences; protected ColumnSelection colSel = new ColumnSelection(); @@ -562,12 +552,11 @@ public abstract class AlignmentViewport implements AlignViewportI, protected ColourSchemeI globalColourScheme = null; - @Override public void setGlobalColourScheme(ColourSchemeI cs) { // TODO: logic refactored from AlignFrame changeColour - - // autorecalc stuff should be changed to rely on the worker system + // TODO: autorecalc stuff should be changed to rely on the worker system // check to see if we should implement a changeColour(cs) method rather than // put th logic in here // - means that caller decides if they want to just modify state and defer @@ -639,7 +628,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } } } - } @Override @@ -988,7 +976,6 @@ public abstract class AlignmentViewport implements AlignViewportI, */ public boolean sortByTree = false; - /** * * @@ -1064,12 +1051,10 @@ public abstract class AlignmentViewport implements AlignViewportI, // hasHiddenColumns = colSel.hasHiddenColumns(); } - protected boolean hasHiddenRows = false; - @Override public boolean hasHiddenRows() { - return hasHiddenRows; + return alignment.getHiddenSequences().getSize() > 0; } protected SequenceGroup selectionGroup; @@ -1308,7 +1293,6 @@ public abstract class AlignmentViewport implements AlignViewportI, setSequenceAnnotationsVisible(seq, true); } - hasHiddenRows = false; hiddenRepSequences = null; firePropertyChange("alignment", null, alignment.getSequences()); @@ -1321,8 +1305,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public void showSequence(int index) { List tmp = alignment.getHiddenSequences().showSequence( - index, - hiddenRepSequences); + index, hiddenRepSequences); if (tmp.size() > 0) { if (selectionGroup == null) @@ -1336,12 +1319,6 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.addSequence(seq, false); setSequenceAnnotationsVisible(seq, true); } - // JBPNote: refactor: only update flag if we modified visiblity (used to - // do this regardless) - if (alignment.getHiddenSequences().getSize() < 1) - { - hasHiddenRows = false; - } firePropertyChange("alignment", null, alignment.getSequences()); sendSelection(); } @@ -1370,7 +1347,6 @@ public abstract class AlignmentViewport implements AlignViewportI, alignment.getHiddenSequences().hideSequence(seq[i]); setSequenceAnnotationsVisible(seq[i], false); } - hasHiddenRows = true; firePropertyChange("alignment", null, alignment.getSequences()); } } @@ -1430,8 +1406,9 @@ public abstract class AlignmentViewport implements AlignViewportI, public boolean isHiddenRepSequence(SequenceI seq) { - return alignment.getSeqrep()==seq || (hiddenRepSequences != null - && hiddenRepSequences.containsKey(seq)); + return alignment.getSeqrep() == seq + || (hiddenRepSequences != null && hiddenRepSequences + .containsKey(seq)); } public SequenceGroup getRepresentedSequences(SequenceI seq) @@ -1453,7 +1430,6 @@ public abstract class AlignmentViewport implements AlignViewportI, colSel.invertColumnSelection(0, alignment.getWidth()); } - @Override public SequenceI[] getSelectionAsNewSequence() { @@ -1481,7 +1457,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return sequences; } - @Override public SequenceI[] getSequenceSelection() { @@ -1497,16 +1472,13 @@ public abstract class AlignmentViewport implements AlignViewportI, return sequences; } - @Override - public CigarArray getViewAsCigars( - boolean selectedRegionOnly) + public CigarArray getViewAsCigars(boolean selectedRegionOnly) { return new CigarArray(alignment, colSel, (selectedRegionOnly ? selectionGroup : null)); } - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) @@ -1514,7 +1486,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return getAlignmentView(selectedOnly, false); } - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly, boolean markGroups) @@ -1524,7 +1495,6 @@ public abstract class AlignmentViewport implements AlignViewportI, markGroups); } - @Override public String[] getViewAsString(boolean selectedRegionOnly) { @@ -1562,7 +1532,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return selection; } - @Override public List getVisibleRegionBoundaries(int min, int max) { @@ -1590,8 +1559,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } } - regions.add(new int[] - { start, end }); + regions.add(new int[] { start, end }); if (colSel != null && colSel.hasHiddenColumns()) { @@ -1606,19 +1574,23 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public List getVisibleAlignmentAnnotation(boolean selectedOnly) + public List getVisibleAlignmentAnnotation( + boolean selectedOnly) { ArrayList ala = new ArrayList(); AlignmentAnnotation[] aa; - if ((aa=alignment.getAlignmentAnnotation())!=null) + if ((aa = alignment.getAlignmentAnnotation()) != null) { - for (AlignmentAnnotation annot:aa) + for (AlignmentAnnotation annot : aa) { AlignmentAnnotation clone = new AlignmentAnnotation(annot); - if (selectedOnly && selectionGroup!=null) + if (selectedOnly && selectionGroup != null) + { + colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), + selectionGroup.getEndRes(), clone); + } + else { - colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone); - } else { colSel.makeVisibleAnnotation(clone); } ala.add(clone); @@ -1627,14 +1599,12 @@ public abstract class AlignmentViewport implements AlignViewportI, return ala; } - @Override public boolean isPadGaps() { return padGaps; } - @Override public void setPadGaps(boolean padGaps) { @@ -1962,6 +1932,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } oldrfs.clear(); } + @Override public boolean isDisplayReferenceSeq() { @@ -2070,7 +2041,8 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public boolean areFeaturesDisplayed() { - return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0; + return featuresDisplayed != null + && featuresDisplayed.getRegisterdFeaturesCount() > 0; } /** @@ -2084,6 +2056,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { viewStyle.setShowSequenceFeatures(b); } + @Override public boolean isShowSequenceFeatures() { @@ -2093,7 +2066,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public void setShowSequenceFeaturesHeight(boolean selected) { - viewStyle.setShowSeqFeaturesHeight(selected); + viewStyle.setShowSequenceFeaturesHeight(selected); } @Override @@ -2102,8 +2075,6 @@ public abstract class AlignmentViewport implements AlignViewportI, return viewStyle.isShowSequenceFeaturesHeight(); } - - @Override public void setShowAnnotation(boolean b) { @@ -2193,14 +2164,6 @@ public abstract class AlignmentViewport implements AlignViewportI, { return viewStyle.isShowColourText(); } - /** - * @return - * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight() - */ - public boolean isShowSeqFeaturesHeight() - { - return viewStyle.isShowSeqFeaturesHeight(); - } /** * @param conservationColourSelected @@ -2356,7 +2319,8 @@ public abstract class AlignmentViewport implements AlignViewportI, protected void broadcastCommand(CommandI command, boolean undo) { - getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource()); + getStructureSelectionManager().commandPerformed(command, undo, + getVamsasSource()); } /** @@ -2527,21 +2491,21 @@ public abstract class AlignmentViewport implements AlignViewportI, */ protected int findComplementScrollTarget(SearchResults sr) { - final AlignViewportI codingComplement = getCodingComplement(); - if (codingComplement == null || !codingComplement.isFollowHighlight()) + final AlignViewportI complement = getCodingComplement(); + if (complement == null || !complement.isFollowHighlight()) { return 0; } boolean iAmProtein = !getAlignment().isNucleotide(); - AlignmentI proteinAlignment = iAmProtein ? getAlignment() - : codingComplement.getAlignment(); + AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement + .getAlignment(); if (proteinAlignment == null) { return 0; } final Set mappings = proteinAlignment .getCodonFrames(); - + /* * Heuristic: find the first mapped sequence (if any) with a non-gapped * residue in the middle column of the visible region. Scroll the @@ -2557,7 +2521,13 @@ public abstract class AlignmentViewport implements AlignViewportI, int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2; final HiddenSequences hiddenSequences = getAlignment() .getHiddenSequences(); - for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++) + + /* + * searching to the bottom of the alignment gives smoother scrolling across + * all gapped visible regions + */ + int lastSeq = alignment.getHeight() - 1; + for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) @@ -2575,7 +2545,7 @@ public abstract class AlignmentViewport implements AlignViewportI, break; } } - + if (sequence == null) { /*