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JAL-2629 add option to set HMM Logo letter height to info content
[jalview.git]
/
src
/
jalview
/
gui
/
CrossRefAction.java
diff --git
a/src/jalview/gui/CrossRefAction.java
b/src/jalview/gui/CrossRefAction.java
index
cb315d6
..
01ee1ff
100644
(file)
--- a/
src/jalview/gui/CrossRefAction.java
+++ b/
src/jalview/gui/CrossRefAction.java
@@
-37,6
+37,8
@@
import jalview.ws.SequenceFetcher;
import java.util.ArrayList;
import java.util.List;
import java.util.ArrayList;
import java.util.List;
+import javax.swing.JOptionPane;
+
/**
* Factory constructor and runnable for discovering and displaying
* cross-references for a set of aligned sequences
/**
* Factory constructor and runnable for discovering and displaying
* cross-references for a set of aligned sequences
@@
-65,10
+67,9
@@
public class CrossRefAction implements Runnable
public void run()
{
final long sttime = System.currentTimeMillis();
public void run()
{
final long sttime = System.currentTimeMillis();
- alignFrame.setProgressBar(
- MessageManager.formatMessage(
- "status.searching_for_sequences_from",
- new Object[] { source }), sttime);
+ alignFrame.setProgressBar(MessageManager.formatMessage(
+ "status.searching_for_sequences_from", new Object[]
+ { source }), sttime);
try
{
AlignmentI alignment = alignFrame.getViewport().getAlignment();
try
{
AlignmentI alignment = alignFrame.getViewport().getAlignment();
@@
-83,8
+84,8
@@
public class CrossRefAction implements Runnable
+ " now searching for " + (dna ? "DNA" : "Protein")
+ " Context.");
}
+ " now searching for " + (dna ? "DNA" : "Protein")
+ " Context.");
}
- AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
- source, dna);
+ AlignmentI xrefs = new CrossRef(sel, dataset)
+ .findXrefSequences(source, dna);
if (xrefs == null)
{
return;
if (xrefs == null)
{
return;
@@
-119,6
+120,10
@@
public class CrossRefAction implements Runnable
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
+ JvOptionPane.showMessageDialog(alignFrame,
+ MessageManager.getString("label.cant_map_cds"),
+ MessageManager.getString("label.operation_failed"),
+ JvOptionPane.OK_OPTION);
System.err.println("Failed to make CDS alignment");
}
System.err.println("Failed to make CDS alignment");
}
@@
-153,8
+158,8
@@
public class CrossRefAction implements Runnable
if (copyAlignment.getHeight() <= 0)
{
if (copyAlignment.getHeight() <= 0)
{
- System.err.println("No Sequences generated for xRef type "
- + source);
+ System.err.println(
+ "No Sequences generated for xRef type " + source);
return;
}
/*
return;
}
/*
@@
-186,8
+191,9
@@
public class CrossRefAction implements Runnable
{
newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
{
newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
- String newtitle = String.format("%s %s %s", MessageManager
- .getString(dna ? "label.proteins" : "label.nucleotides"),
+ String newtitle = String.format("%s %s %s",
+ dna ? MessageManager.getString("label.proteins")
+ : MessageManager.getString("label.nucleotides"),
MessageManager.getString("label.for"), alignFrame.getTitle());
newFrame.setTitle(newtitle);
MessageManager.getString("label.for"), alignFrame.getTitle());
newFrame.setTitle(newtitle);
@@
-251,8
+257,8
@@
public class CrossRefAction implements Runnable
} finally
{
alignFrame.setProgressBar(MessageManager.formatMessage(
} finally
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.finished_searching_for_sequences_from",
- new Object[] { source }), sttime);
+ "status.finished_searching_for_sequences_from", new Object[]
+ { source }), sttime);
}
}
}
}
@@
-273,9
+279,8
@@
public class CrossRefAction implements Runnable
for (int s = 0; s < sprods.length; s++)
{
sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
for (int s = 0; s < sprods.length; s++)
{
sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
- if (dataset.getSequences() == null
- || !dataset.getSequences().contains(
- sprods[s].getDatasetSequence()))
+ if (dataset.getSequences() == null || !dataset.getSequences()
+ .contains(sprods[s].getDatasetSequence()))
{
dataset.addSequence(sprods[s].getDatasetSequence());
}
{
dataset.addSequence(sprods[s].getDatasetSequence());
}