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JAL-2759 Refactor of hideInsertionsFor after review
author
kiramt
<k.mourao@dundee.ac.uk>
Mon, 15 Jan 2018 13:32:35 +0000
(13:32 +0000)
committer
kiramt
<k.mourao@dundee.ac.uk>
Mon, 15 Jan 2018 13:32:35 +0000
(13:32 +0000)
src/jalview/bin/JalviewLite.java
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src/jalview/datamodel/Alignment.java
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src/jalview/datamodel/AlignmentI.java
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src/jalview/datamodel/HiddenColumns.java
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src/jalview/gui/AlignFrame.java
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src/jalview/io/AnnotationFile.java
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test/jalview/datamodel/HiddenColumnsTest.java
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diff --git
a/src/jalview/bin/JalviewLite.java
b/src/jalview/bin/JalviewLite.java
index
6504290
..
a60496c
100644
(file)
--- a/
src/jalview/bin/JalviewLite.java
+++ b/
src/jalview/bin/JalviewLite.java
@@
-31,7
+31,6
@@
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
@@
-471,7
+470,7
@@
public class JalviewLite extends Applet
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
+ List<Integer> cs = new ArrayList<>(csel.getSelected());
csel.clear();
for (Integer selectedCol : cs)
{
csel.clear();
for (Integer selectedCol : cs)
{
@@
-921,7
+920,7
@@
public class JalviewLite extends Applet
setMouseoverListener(currentAlignFrame, listener);
}
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<>();
/*
* (non-Javadoc)
/*
* (non-Javadoc)
@@
-2165,8
+2164,8
@@
public class JalviewLite extends Applet
else
{
param = st.nextToken();
else
{
param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
- List<String> tmp2 = new ArrayList<String>();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> tmp2 = new ArrayList<>();
while (st.hasMoreTokens())
{
while (st.hasMoreTokens())
{
@@
-2279,12
+2278,9
@@
public class JalviewLite extends Applet
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
// false == do not add sequence profile from concise output
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
// false == do not add sequence profile from concise output
- SequenceI repseq = alignFrame.viewport.getAlignment()
- .getSequenceAt(0);
- alignFrame.viewport.getAlignment().setSeqrep(repseq);
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq);
- alignFrame.viewport.getAlignment().setHiddenColumns(cs);
+
+ alignFrame.viewport.getAlignment().setupJPredAlignment();
+
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
@@
-2802,9
+2798,9
@@
public class JalviewLite extends Applet
// callInitCallback();
}
// callInitCallback();
}
- private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
+ private Hashtable<String, long[]> jshashes = new Hashtable<>();
- private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
public void setJsMessageSet(String messageclass, String viewId,
String[] colcommands)
public void setJsMessageSet(String messageclass, String viewId,
String[] colcommands)
@@
-2812,7
+2808,7
@@
public class JalviewLite extends Applet
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
if (msgset == null)
{
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
if (msgset == null)
{
- msgset = new Hashtable<String, String[]>();
+ msgset = new Hashtable<>();
jsmessages.put(messageclass, msgset);
}
msgset.put(viewId, colcommands);
jsmessages.put(messageclass, msgset);
}
msgset.put(viewId, colcommands);
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
8c5e4ac
..
f052c05
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-1913,4
+1913,14
@@
public class Alignment implements AlignmentI
{
hiddenCols = cols;
}
{
hiddenCols = cols;
}
+
+ @Override
+ public void setupJPredAlignment()
+ {
+ SequenceI repseq = getSequenceAt(0);
+ setSeqrep(repseq);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideInsertionsFor(repseq.getInsertions());
+ setHiddenColumns(cs);
+ }
}
}
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
084b80e
..
bdc48d0
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-580,6
+580,17
@@
public interface AlignmentI extends AnnotatedCollectionI
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
*/
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+ /**
+ * Set the hidden columns collection on the alignment
+ *
+ * @param cols
+ */
public void setHiddenColumns(HiddenColumns cols);
public void setHiddenColumns(HiddenColumns cols);
+ /**
+ * Set the first sequence as representative and hide its insertions. Typically
+ * used when loading JPred files.
+ */
+ public void setupJPredAlignment();
+
}
}
diff --git
a/src/jalview/datamodel/HiddenColumns.java
b/src/jalview/datamodel/HiddenColumns.java
index
d1345e3
..
2b5185f
100644
(file)
--- a/
src/jalview/datamodel/HiddenColumns.java
+++ b/
src/jalview/datamodel/HiddenColumns.java
@@
-303,14
+303,13
@@
public class HiddenColumns
* mark the columns corresponding to gap characters as hidden in the column
* selection
*
* mark the columns corresponding to gap characters as hidden in the column
* selection
*
- * @param sr
+ * @param insertions
*/
*/
- public void hideInsertionsFor(SequenceI sr)
+ public void hideInsertionsFor(List<int[]> inserts)
{
try
{
LOCK.writeLock().lock();
{
try
{
LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
for (int[] r : inserts)
{
hideColumns(r[0], r[1]);
for (int[] r : inserts)
{
hideColumns(r[0], r[1]);
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
fa052f1
..
0c452c3
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-4627,11
+4627,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
- SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
- viewport.getAlignment().setSeqrep(repseq);
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq);
- viewport.getAlignment().setHiddenColumns(cs);
+ viewport.getAlignment().setupJPredAlignment();
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
00476d6
..
885a298
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-968,7
+968,7
@@
public class AnnotationFile
else
{
// consider deferring this till after the file has been parsed ?
else
{
// consider deferring this till after the file has been parsed ?
- hidden.hideInsertionsFor(sr);
+ hidden.hideInsertionsFor(sr.getInsertions());
}
}
modified = true;
}
}
modified = true;
diff --git
a/test/jalview/datamodel/HiddenColumnsTest.java
b/test/jalview/datamodel/HiddenColumnsTest.java
index
ba2c1ea
..
a31d527
100644
(file)
--- a/
test/jalview/datamodel/HiddenColumnsTest.java
+++ b/
test/jalview/datamodel/HiddenColumnsTest.java
@@
-420,7
+420,7
@@
public class HiddenColumnsTest
new SequenceI[]
{ new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
HiddenColumns cs = new HiddenColumns();
new SequenceI[]
{ new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(al.getSequenceAt(0));
+ cs.hideInsertionsFor(al.getSequenceAt(0).getInsertions());
assertEquals("G", ""
+ al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9)));
assertEquals("G", ""
+ al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9)));
@@
-1139,10
+1139,10
@@
public class HiddenColumnsTest
SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
- h.hideInsertionsFor(seq2);
+ h.hideInsertionsFor(seq2.getInsertions());
assertTrue(h.equals(h2));
assertTrue(h.equals(h2));
- h.hideInsertionsFor(seq1);
+ h.hideInsertionsFor(seq1.getInsertions());
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
h2.hideColumns(19, 20);
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
h2.hideColumns(19, 20);