package jalview.bin;
-import jalview.api.AlignFrameI;
import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.Alignment;
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.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
return arrayToSeparatorList(array, separator);
}
- public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)
{
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
sep = separator; // "+0x00AC;
}
- AlignViewport v = ((AlignFrame) alf).getViewport();
+ AlignViewport v = alf.getViewport();
if (v.getSelectionGroup() != null)
{
SequenceI[] seqs = v.getSelectionGroup()
return result.toString();
}
- public void setFeatureGroupStateOn(final AlignFrameI alf,
+ public void setFeatureGroupStateOn(final AlignFrame alf,
final String groups, boolean state)
{
java.awt.EventQueue.invokeLater(new Runnable()
@Override
public void run()
{
- ((AlignFrame) alf).setFeatureGroupState(
+ alf.setFeatureGroupState(
separatorListToArray(groups, separator), state);
}
});
}
- public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
return arrayToSeparatorList(
- ((AlignFrame) alf).getFeatureGroupsOfState(visible));
+ alf.getFeatureGroupsOfState(visible));
}
- public void scrollViewToIn(final AlignFrameI alf, final String topRow,
+ public void scrollViewToIn(final AlignFrame alf, final String topRow,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- ((AlignFrame) alf).scrollTo(new Integer(topRow).intValue(),
- new Integer(leftHandColumn).intValue());
+ alf.scrollTo(Integer.valueOf(topRow).intValue(),
+ Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
});
}
- public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- ((AlignFrame) alf).scrollToRow(new Integer(topRow).intValue());
+ alf.scrollToRow(Integer.valueOf(topRow).intValue());
} catch (Exception ex)
{
});
}
- public void scrollViewToColumnIn(final AlignFrameI alf,
+ public void scrollViewToColumnIn(final AlignFrame alf,
final String leftHandColumn)
{
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- ((AlignFrame) alf)
- .scrollToColumn(new Integer(leftHandColumn).intValue());
+ alf
+ .scrollToColumn(
+ Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
}
- public boolean addPdbFile(AlignFrameI alf, String sequenceId,
+ public boolean addPdbFile(AlignFrame alf, String sequenceId,
String pdbEntryString, String pdbFile)
{
- AlignFrame alFrame = (AlignFrame) alf;
+ AlignFrame alFrame = alf;
SequenceI toaddpdb = alFrame.getViewport().getAlignment()
.findName(sequenceId);
boolean needtoadd = false;
return true;
}
- public AlignFrameI loadAlignment(String text, int width, int height,
+ public AlignFrame loadAlignment(String text, int width, int height,
String title)
{
AlignmentI al = null;
return null;
}
- public String getFeatureGroupsOn(AlignFrameI alf)
+ public String getFeatureGroupsOn(AlignFrame alf)
{
return arrayToSeparatorList(
- ((AlignFrame) alf).getFeatureGroups());
+ alf.getFeatureGroups());
}
- public void highlightIn(final AlignFrameI alf, final String sequenceId,
+ public void highlightIn(final AlignFrame alf, final String sequenceId,
final String position, final String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- ((AlignFrame) alf).getViewport().getAlignment()
+ alf.getViewport().getAlignment()
.getSequencesArray());
final SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
int apos = -1;
try
{
- apos = new Integer(position).intValue();
+ apos = Integer.valueOf(position).intValue();
apos--;
} catch (NumberFormatException ex)
{
}
}
- public void selectIn(final AlignFrameI alf, String sequenceIds,
+ public void selectIn(final AlignFrame alf, String sequenceIds,
String columns, String sep)
{
if (sep == null || sep.length() == 0)
String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
- AlignmentI al = ((AlignFrame) alf).getViewport().getAlignment();
+ AlignmentI al = alf.getViewport().getAlignment();
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- ((AlignFrame) alf).getViewport().getAlignment()
+ alf.getViewport().getAlignment()
.getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
int from = -1, to = -1;
try
{
- from = new Integer(cl.substring(0, p)).intValue();
+ from = Integer.valueOf(cl.substring(0, p)).intValue();
from--;
} catch (NumberFormatException ex)
{
}
try
{
- to = new Integer(cl.substring(p + 1)).intValue();
+ to = Integer.valueOf(cl.substring(p + 1)).intValue();
to--;
} catch (NumberFormatException ex)
{
int r = -1;
try
{
- r = new Integer(cl).intValue();
+ r = Integer.valueOf(cl).intValue();
r--;
} catch (NumberFormatException ex)
{
@Override
public void run()
{
- ((AlignFrame) alf).select(sel, csel, ((AlignFrame) alf)
+ alf.select(sel, csel, alf
.getCurrentView().getAlignment().getHiddenColumns());
}
});
}
}
- public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
{
- AlignmentI alorder = ((AlignFrame) alf).getViewport().getAlignment();
+ AlignmentI alorder = alf.getViewport().getAlignment();
String[] order = new String[alorder.getHeight()];
for (int i = 0; i < order.length; i++)
{
return arrayToSeparatorList(order, sep);
}
- public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix)
{
try
{
- AlignViewport vp = ((AlignFrame) alf).getViewport();
+ AlignViewport vp = alf.getViewport();
FileFormatI theFormat = FileFormats.getInstance().forName(format);
boolean seqlimits = (suffix == null
|| suffix.equalsIgnoreCase("true"));
return "";
}
- public String orderAlignmentBy(AlignFrameI alf, String order,
+ public String orderAlignmentBy(AlignFrame alf, String order,
String undoName, String sep)
{
if (sep == null || sep.length() == 0)
if (ids != null && ids.length > 0)
{
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- ((AlignFrame) alf).getViewport().getAlignment()
+ alf.getViewport().getAlignment()
.getSequencesArray());
int s = 0;
sqs = new SequenceI[ids.length];
final String _undoName = undoName;
// TODO: deal with synchronization here: cannot raise any events until after
// this has returned.
- return ((AlignFrame) alf).sortBy(aorder, _undoName) ? "true" : "";
+ return alf.sortBy(aorder, _undoName) ? "true" : "";
}
- public String getAlignmentFrom(AlignFrameI alf, String format,
+ public String getAlignmentFrom(AlignFrame alf, String format,
String suffix)
{
try
FileFormatI theFormat = FileFormats.getInstance().forName(format);
String reply = new AppletFormatAdapter().formatSequences(theFormat,
- ((AlignFrame) alf).getViewport().getAlignment(), seqlimits);
+ alf.getViewport().getAlignment(), seqlimits);
return reply;
} catch (IllegalArgumentException ex)
{
}
}
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
+ if (new AnnotationFile().annotateAlignmentView(
+ alf.getViewport(), annotation,
+ DataSourceType.PASTE))
+ {
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ alf.parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
+ }
+ }
+
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ boolean autoenabledisplay)
+ {
+ boolean ret = alf.parseFeaturesFile(features,
+ DataSourceType.PASTE);
+ if (!ret)
+ {
+ return false;
+ }
+ if (autoenabledisplay)
+ {
+ alf.getViewport().setShowSequenceFeatures(true);
+ // this next was for a checkbox in JalviewLite
+ // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+ }
+ return true;
+ }
+
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ AlignFrame f = (alf);
+
+ String features;
+ FeaturesFile formatter = new FeaturesFile();
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ features = formatter.printJalviewFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(), true);
+ }
+ else
+ {
+ features = formatter.printGffFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(), true);
+ }
+
+ if (features == null)
+ {
+ features = "";
+ }
+ return features;
+
+ }
+
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ AlignFrame f = alf;
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(f.getViewport());
+ return annotation;
+ }
+
+ // public AlignFrame newViewFrom(AlignFrame alf, String name)
+ // {
+ // return (AlignFrame) alf.newView(name, true);
+ // }
+ //
+ public String[] separatorListToArray(String list)
+ {
+ return separatorListToArray(list, separator);
+ }
+
+ public Object[] getSelectionForListener(AlignFrame currentFrame,
+ SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof AlignViewport
+ && currentFrame.getViewport() == source)
+ {
+ // should be valid if it just generated an event!
+ src = currentFrame;
+
+ }
+ }
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ seqs = new String[seqsel.getSize()];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = seqsel.getSequenceAt(i).getName();
+ }
+ if (strt < seqsel.getStartRes())
+ {
+ strt = seqsel.getStartRes();
+ }
+ if (end == -1 || end > seqsel.getEndRes())
+ {
+ end = seqsel.getEndRes();
+ }
+ }
+ if (colsel != null && !colsel.isEmpty())
+ {
+ if (end == -1)
+ {
+ end = colsel.getMax() + 1;
+ }
+ cols = new String[colsel.getSelected().size()];
+ for (int i = 0; i < cols.length; i++)
+ {
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ }
+ }
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[2];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ return new Object[] { src, setid, arrayToSeparatorList(seqs),
+ arrayToSeparatorList(cols) };
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff