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JAL-1925 update source version in license
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
5617bcf
..
65567dc
100644
(file)
--- 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-540,7
+540,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
return isDataset;
}
return isDataset;
}
-
private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
protected ColumnSelection colSel = new ColumnSelection();
private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
protected ColumnSelection colSel = new ColumnSelection();
@@
-553,12
+552,11
@@
public abstract class AlignmentViewport implements AlignViewportI,
protected ColourSchemeI globalColourScheme = null;
protected ColourSchemeI globalColourScheme = null;
-
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
// TODO: logic refactored from AlignFrame changeColour -
@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
// 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
@@
-630,7
+628,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
}
}
}
}
}
-
}
@Override
}
@Override
@@
-979,7
+976,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
*/
public boolean sortByTree = false;
*/
public boolean sortByTree = false;
-
/**
*
*
/**
*
*
@@
-1061,7
+1057,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
return alignment.getHiddenSequences().getSize() > 0;
}
return alignment.getHiddenSequences().getSize() > 0;
}
-
protected SequenceGroup selectionGroup;
public void setSequenceSetId(String newid)
protected SequenceGroup selectionGroup;
public void setSequenceSetId(String newid)
@@
-1310,8
+1305,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void showSequence(int index)
{
List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
public void showSequence(int index)
{
List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
- index,
- hiddenRepSequences);
+ index, hiddenRepSequences);
if (tmp.size() > 0)
{
if (selectionGroup == null)
if (tmp.size() > 0)
{
if (selectionGroup == null)
@@
-1412,8
+1406,9
@@
public abstract class AlignmentViewport implements AlignViewportI,
public boolean isHiddenRepSequence(SequenceI seq)
{
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)
}
public SequenceGroup getRepresentedSequences(SequenceI seq)
@@
-1435,7
+1430,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
colSel.invertColumnSelection(0, alignment.getWidth());
}
colSel.invertColumnSelection(0, alignment.getWidth());
}
-
@Override
public SequenceI[] getSelectionAsNewSequence()
{
@Override
public SequenceI[] getSelectionAsNewSequence()
{
@@
-1463,7
+1457,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
return sequences;
}
return sequences;
}
-
@Override
public SequenceI[] getSequenceSelection()
{
@Override
public SequenceI[] getSequenceSelection()
{
@@
-1479,16
+1472,13
@@
public abstract class AlignmentViewport implements AlignViewportI,
return sequences;
}
return sequences;
}
-
@Override
@Override
- public CigarArray getViewAsCigars(
- boolean selectedRegionOnly)
+ public CigarArray getViewAsCigars(boolean selectedRegionOnly)
{
return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
{
return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
-
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
@@
-1496,7
+1486,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
return getAlignmentView(selectedOnly, false);
}
return getAlignmentView(selectedOnly, false);
}
-
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
@@
-1506,7
+1495,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
markGroups);
}
markGroups);
}
-
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
@@
-1544,7
+1532,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
return selection;
}
return selection;
}
-
@Override
public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
@Override
public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
@@
-1572,8
+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())
{
if (colSel != null && colSel.hasHiddenColumns())
{
@@
-1588,19
+1574,23
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
@Override
}
@Override
- public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+ public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+ boolean selectedOnly)
{
ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
AlignmentAnnotation[] aa;
{
ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
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);
{
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);
colSel.makeVisibleAnnotation(clone);
}
ala.add(clone);
@@
-1609,14
+1599,12
@@
public abstract class AlignmentViewport implements AlignViewportI,
return ala;
}
return ala;
}
-
@Override
public boolean isPadGaps()
{
return padGaps;
}
@Override
public boolean isPadGaps()
{
return padGaps;
}
-
@Override
public void setPadGaps(boolean padGaps)
{
@Override
public void setPadGaps(boolean padGaps)
{
@@
-1944,6
+1932,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
oldrfs.clear();
}
}
oldrfs.clear();
}
+
@Override
public boolean isDisplayReferenceSeq()
{
@Override
public boolean isDisplayReferenceSeq()
{
@@
-2052,7
+2041,8
@@
public abstract class AlignmentViewport implements AlignViewportI,
@Override
public boolean areFeaturesDisplayed()
{
@Override
public boolean areFeaturesDisplayed()
{
- return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+ return featuresDisplayed != null
+ && featuresDisplayed.getRegisterdFeaturesCount() > 0;
}
/**
}
/**
@@
-2066,6
+2056,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
{
viewStyle.setShowSequenceFeatures(b);
}
{
viewStyle.setShowSequenceFeatures(b);
}
+
@Override
public boolean isShowSequenceFeatures()
{
@Override
public boolean isShowSequenceFeatures()
{
@@
-2084,8
+2075,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
return viewStyle.isShowSequenceFeaturesHeight();
}
return viewStyle.isShowSequenceFeaturesHeight();
}
-
-
@Override
public void setShowAnnotation(boolean b)
{
@Override
public void setShowAnnotation(boolean b)
{
@@
-2330,7
+2319,8
@@
public abstract class AlignmentViewport implements AlignViewportI,
protected void broadcastCommand(CommandI command, boolean undo)
{
protected void broadcastCommand(CommandI command, boolean undo)
{
- getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
+ getStructureSelectionManager().commandPerformed(command, undo,
+ getVamsasSource());
}
/**
}
/**
@@
-2501,21
+2491,21
@@
public abstract class AlignmentViewport implements AlignViewportI,
*/
protected int findComplementScrollTarget(SearchResults sr)
{
*/
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();
{
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<AlignedCodonFrame> mappings = proteinAlignment
.getCodonFrames();
if (proteinAlignment == null)
{
return 0;
}
final Set<AlignedCodonFrame> 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
/*
* Heuristic: find the first mapped sequence (if any) with a non-gapped
* residue in the middle column of the visible region. Scroll the
@@
-2531,7
+2521,13
@@
public abstract class AlignmentViewport implements AlignViewportI,
int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
final HiddenSequences hiddenSequences = getAlignment()
.getHiddenSequences();
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))
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@
-2549,7
+2545,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
break;
}
}
break;
}
}
-
+
if (sequence == null)
{
/*
if (sequence == null)
{
/*