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Input Data...
[jalview.git]
/
src
/
jalview
/
ws
/
MsaWSClient.java
diff --git
a/src/jalview/ws/MsaWSClient.java
b/src/jalview/ws/MsaWSClient.java
index
999fc96
..
49c879b
100755
(executable)
--- a/
src/jalview/ws/MsaWSClient.java
+++ b/
src/jalview/ws/MsaWSClient.java
@@
-58,7
+58,7
@@
public class MsaWSClient
*/
\r
\r
public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
\r
*/
\r
\r
public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
\r
- SequenceI[] msa,
\r
+ jalview.datamodel.AlignmentView msa,
\r
boolean submitGaps, boolean preserveOrder,
\r
Alignment seqdataset,
\r
AlignFrame _alignFrame)
\r
boolean submitGaps, boolean preserveOrder,
\r
Alignment seqdataset,
\r
AlignFrame _alignFrame)
\r
@@
-91,7
+91,7
@@
public class MsaWSClient
}
\r
\r
\r
}
\r
\r
\r
- private void startMsaWSClient(String altitle, SequenceI[] msa,
\r
+ private void startMsaWSClient(String altitle, AlignmentView msa,
\r
boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
\r
{
\r
if (!locateWebService())
\r
boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
\r
{
\r
if (!locateWebService())
\r
@@
-141,6
+141,16
@@
public class MsaWSClient
return true;
\r
}
\r
\r
return true;
\r
}
\r
\r
+ protected String getServiceActionKey()
\r
+ {
\r
+ return "MsaWS";
\r
+ }
\r
+
\r
+ protected String getServiceActionDescription()
\r
+ {
\r
+ return "Multiple Sequence Alignment";
\r
+ }
\r
+
\r
protected class MsaWSThread
\r
extends Thread implements WSClientI
\r
{
\r
protected class MsaWSThread
\r
extends Thread implements WSClientI
\r
{
\r
@@
-159,33
+169,34
@@
public class MsaWSClient
\r
Alignment dataset; // dataset to which the new alignment will be associated.
\r
\r
\r
Alignment dataset; // dataset to which the new alignment will be associated.
\r
\r
- MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
\r
+ MsaWSThread(String title, AlignmentView _msa, boolean subgaps,
\r
boolean presorder, Alignment seqset)
\r
{
\r
boolean presorder, Alignment seqset)
\r
{
\r
+ // jbpnote - transformation should be above here - this is per sequence set contig, not for many contigs.
\r
alTitle = title;
\r
submitGaps = subgaps;
\r
preserveOrder = presorder;
\r
dataset = seqset;
\r
OutputHeader = wsInfo.getProgressText();
\r
SeqNames = new Hashtable();
\r
alTitle = title;
\r
submitGaps = subgaps;
\r
preserveOrder = presorder;
\r
dataset = seqset;
\r
OutputHeader = wsInfo.getProgressText();
\r
SeqNames = new Hashtable();
\r
-
\r
+ SeqCigar[] msa = _msa.getSequences();
\r
vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
\r
Sequence[msa.length];
\r
\r
vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
\r
Sequence[msa.length];
\r
\r
- for (int i = 0; i < msa.length; i++)
\r
+ for (int i = 0,n=0; i < msa.length; i++)
\r
{
\r
String newname = jalview.analysis.SeqsetUtils.unique_name(i);
\r
{
\r
String newname = jalview.analysis.SeqsetUtils.unique_name(i);
\r
-
\r
+ SequenceI mseq = msa[i].getSeq('-');
\r
// uniquify as we go
\r
// TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
\r
SeqNames.put(newname,
\r
// uniquify as we go
\r
// TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
\r
SeqNames.put(newname,
\r
- jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
\r
+ jalview.analysis.SeqsetUtils.SeqCharacterHash(mseq));
\r
seqarray[i] = new vamsas.objects.simple.Sequence();
\r
seqarray[i].setId(newname);
\r
seqarray[i] = new vamsas.objects.simple.Sequence();
\r
seqarray[i].setId(newname);
\r
- seqarray[i].setSeq( (submitGaps) ? msa[i].getSequence()
\r
+ seqarray[i].setSeq( (submitGaps) ? mseq.getSequence()
\r
: AlignSeq.extractGaps(
\r
jalview.util.Comparison.GapChars,
\r
: AlignSeq.extractGaps(
\r
jalview.util.Comparison.GapChars,
\r
- msa[i].getSequence()));
\r
+ mseq.getSequence()));
\r
}
\r
\r
this.seqs = new vamsas.objects.simple.SequenceSet();
\r
}
\r
\r
this.seqs = new vamsas.objects.simple.SequenceSet();
\r