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Merge branch 'documentation/JAL-2418_release2102' into develop
[jalview.git]
/
src
/
jalview
/
io
/
AnnotationFile.java
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
5c5fa8f
..
b669ee5
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-110,23
+110,22
@@
public class AnnotationFile
*/
public class ViewDef
{
*/
public class ViewDef
{
- public String viewname;
+ // TODO this class is not used - remove?
+ public final String viewname;
- public HiddenSequences hidseqs;
+ public final HiddenSequences hidseqs;
- public HiddenColumns hiddencols;
+ public final HiddenColumns hiddencols;
- public Vector visibleGroups;
+ public final Hashtable hiddenRepSeqs;
- public Hashtable hiddenRepSeqs;
-
- public ViewDef(String viewname, HiddenSequences hidseqs,
- HiddenColumns hiddencols, Hashtable hiddenRepSeqs)
+ public ViewDef(String vname, HiddenSequences hseqs,
+ HiddenColumns hcols, Hashtable hRepSeqs)
{
{
- this.viewname = viewname;
- this.hidseqs = hidseqs;
- this.hiddencols = hiddencols;
- this.hiddenRepSeqs = hiddenRepSeqs;
+ this.viewname = vname;
+ this.hidseqs = hseqs;
+ this.hiddencols = hcols;
+ this.hiddenRepSeqs = hRepSeqs;
}
}
}
}
@@
-153,7
+152,7
@@
public class AnnotationFile
}
if (list == null)
{
}
if (list == null)
{
- list = view.visibleGroups;
+ // list = view.visibleGroups;
}
if (cs == null)
{
}
if (cs == null)
{
@@
-172,22
+171,9
@@
public class AnnotationFile
if (cs != null && cs.hasHiddenColumns())
{
text.append("VIEW_HIDECOLS\t");
if (cs != null && cs.hasHiddenColumns())
{
text.append("VIEW_HIDECOLS\t");
- List<int[]> hc = cs.getHiddenRegions();
- boolean comma = false;
- for (int[] r : hc)
- {
- if (!comma)
- {
- comma = true;
- }
- else
- {
- text.append(",");
- }
- text.append(r[0]);
- text.append("-");
- text.append(r[1]);
- }
+
+ String regions = cs.regionsToString(",", "-");
+ text.append(regions);
text.append("\n");
}
// TODO: allow efficient recovery of annotation data shown in several
text.append("\n");
}
// TODO: allow efficient recovery of annotation data shown in several
@@
-203,8
+189,8
@@
public class AnnotationFile
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
- Hashtable<Integer, String> graphGroup = new Hashtable<Integer, String>();
- Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer, Object[]>();
+ Hashtable<Integer, String> graphGroup = new Hashtable<>();
+ Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<>();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
@@
-538,7
+524,7
@@
public class AnnotationFile
return false;
}
return false;
}
- public void printGroups(List<SequenceGroup> list)
+ protected void printGroups(List<SequenceGroup> list)
{
SequenceI seqrep = null;
for (SequenceGroup sg : list)
{
SequenceI seqrep = null;
for (SequenceGroup sg : list)
@@
-584,7
+570,8
@@
public class AnnotationFile
if (sg.cs != null)
{
text.append("colour=");
if (sg.cs != null)
{
text.append("colour=");
- text.append(sg.cs.toString());
+ text.append(ColourSchemeProperty.getColourName(sg.cs
+ .getColourScheme()));
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
@@
-748,8
+735,8
@@
public class AnnotationFile
BufferedReader in) throws Exception
{
nlinesread = 0;
BufferedReader in) throws Exception
{
nlinesread = 0;
- ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
- ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<Object[]>();
+ ArrayList<Object[]> combineAnnotation_calls = new ArrayList<>();
+ ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<>();
boolean modified = false;
String groupRef = null;
Hashtable groupRefRows = new Hashtable();
boolean modified = false;
String groupRef = null;
Hashtable groupRefRows = new Hashtable();
@@
-1112,7
+1099,7
@@
public class AnnotationFile
modified = true;
}
// Resolve the groupRefs
modified = true;
}
// Resolve the groupRefs
- Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
+ Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<>();
Enumeration en = groupRefRows.keys();
while (en.hasMoreElements())
Enumeration en = groupRefRows.keys();
while (en.hasMoreElements())