X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=62b723dba3425af6fd5f6500c79e97b9b79b0793;hb=1abd3042358350c391c9a184061a2b7c552f84d1;hp=8328e7ab45b64ffa6f5f1efeafd30d52ad203a09;hpb=5a631296dd1dcc1df7b50487a647c27333696c74;p=jalview.git
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 8328e7a..62b723d 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,7 +20,8 @@
*/
package jalview.io;
-import java.util.Arrays;
+import java.util.Locale;
+
import java.util.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
@@ -58,9 +59,7 @@ public class SequenceAnnotationReport
private static String linkImageURL;
- private static final String[][] PRIMARY_SOURCES = new String[][] {
- DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
- DBRefSource.PROTEINDBS };
+ // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
/*
* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
@@ -82,8 +81,8 @@ public class SequenceAnnotationReport
}
String s1 = ref1.getSource();
String s2 = ref2.getSource();
- boolean s1Primary = isPrimarySource(s1);
- boolean s2Primary = isPrimarySource(s2);
+ boolean s1Primary = DBRefSource.isPrimarySource(s1);
+ boolean s2Primary = DBRefSource.isPrimarySource(s2);
if (s1Primary && !s2Primary)
{
return -1;
@@ -104,20 +103,20 @@ public class SequenceAnnotationReport
return comp;
}
- private boolean isPrimarySource(String source)
- {
- for (String[] primary : PRIMARY_SOURCES)
- {
- for (String s : primary)
- {
- if (source.equals(s))
- {
- return true;
- }
- }
- }
- return false;
- }
+// private boolean isPrimarySource(String source)
+// {
+// for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+// {
+// for (String s : primary)
+// {
+// if (source.equals(s))
+// {
+// return true;
+// }
+// }
+// }
+// return false;
+// }
};
private boolean forTooltip;
@@ -216,6 +215,11 @@ public class SequenceAnnotationReport
{
beginRange = mf.getMappedPositions(begin, begin);
endRange = mf.getMappedPositions(end, end);
+ if (beginRange == null || endRange == null)
+ {
+ // something went wrong
+ return false;
+ }
begin = beginRange[0];
end = endRange[endRange.length - 1];
}
@@ -271,7 +275,7 @@ public class SequenceAnnotationReport
* truncate overlong descriptions unless they contain an href
* before the truncation point (as truncation could leave corrupted html)
*/
- int linkindex = description.toLowerCase().indexOf(" -1
&& linkindex < MAX_DESCRIPTION_LENGTH;
if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
@@ -398,8 +402,8 @@ public class SequenceAnnotationReport
+ "\" target=\""
+ urllink.get(0)
+ "\">"
- + (urllink.get(0).toLowerCase()
- .equals(urllink.get(1).toLowerCase()) ? urllink
+ + (urllink.get(0).toLowerCase(Locale.ROOT)
+ .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
.get(1)))
+ "
");
@@ -517,14 +521,14 @@ public class SequenceAnnotationReport
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- DBRefEntry[] dbrefs = ds.getDBRefs();
+ List dbrefs = ds.getDBRefs();
if (dbrefs == null)
{
return 0;
}
// note this sorts the refs held on the sequence!
- Arrays.sort(dbrefs, comparator);
+ dbrefs.sort(comparator);
boolean ellipsis = false;
String source = null;
String lastSource = null;