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JAL-1645 source formatting and organise imports
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
43af832
..
3f1946e
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-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
@@
-978,7
+976,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
*/
public boolean sortByTree = false;
*/
public boolean sortByTree = false;
-
/**
*
*
/**
*
*
@@
-1060,7
+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)
@@
-1309,8
+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)
@@
-1411,8
+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)
@@
-1434,7
+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()
{
@@
-1462,7
+1457,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
return sequences;
}
return sequences;
}
-
@Override
public SequenceI[] getSequenceSelection()
{
@Override
public SequenceI[] getSequenceSelection()
{
@@
-1478,16
+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)
@@
-1495,7
+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)
@@
-1505,7
+1495,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
markGroups);
}
markGroups);
}
-
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
@@
-1543,7
+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)
{
@@
-1571,8
+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())
{
@@
-1587,19
+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);
@@
-1608,14
+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)
{
@@
-1943,6
+1932,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
oldrfs.clear();
}
}
oldrfs.clear();
}
+
@Override
public boolean isDisplayReferenceSeq()
{
@Override
public boolean isDisplayReferenceSeq()
{
@@
-2051,7
+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;
}
/**
}
/**
@@
-2065,6
+2056,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
{
viewStyle.setShowSequenceFeatures(b);
}
{
viewStyle.setShowSequenceFeatures(b);
}
+
@Override
public boolean isShowSequenceFeatures()
{
@Override
public boolean isShowSequenceFeatures()
{
@@
-2083,8
+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)
{
@@
-2329,7
+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());
}
/**
}
/**
@@
-2506,15
+2497,15
@@
public abstract class AlignmentViewport implements AlignViewportI,
return 0;
}
boolean iAmProtein = !getAlignment().isNucleotide();
return 0;
}
boolean iAmProtein = !getAlignment().isNucleotide();
- AlignmentI proteinAlignment = iAmProtein ? getAlignment()
- : complement.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
@@
-2530,9
+2521,10
@@
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();
-
+
/*
/*
- * searching to the bottom of the alignment gives smoother scrolling across all gapped visible regions
+ * 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++)
*/
int lastSeq = alignment.getHeight() - 1;
for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
@@
-2550,10
+2542,10
@@
public abstract class AlignmentViewport implements AlignViewportI,
.findMappingsForSequence(sequence, mappings);
if (!seqMappings.isEmpty())
{
.findMappingsForSequence(sequence, mappings);
if (!seqMappings.isEmpty())
{
- break;
+ break;
}
}
}
}
-
+
if (sequence == null)
{
/*
if (sequence == null)
{
/*