import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
+import jalview.io.FileFormat;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
{
viewport.setColumnSelection(columnSelection);
}
+ viewport.setScaleAboveWrapped(scaleAbove.getState());
alignPanel = new AlignmentPanel(this, viewport);
avc = new jalview.controller.AlignViewController(this, viewport,
* is protocol for accessing data referred to by file
*/
- public boolean parseFeaturesFile(String file, String type)
+ public boolean parseFeaturesFile(String file, DataSourceType type)
{
return parseFeaturesFile(file, type, true);
}
*
* @param file
* file URL, content, or other resolvable path
- * @param type
+ * @param paste
* is protocol for accessing data referred to by file
* @param autoenabledisplay
* when true, display features flag will be automatically enabled if
* features are loaded
* @return true if data parsed as a features file
*/
- public boolean parseFeaturesFile(String file, String type,
+ public boolean parseFeaturesFile(String file, DataSourceType paste,
boolean autoenabledisplay)
{
- // TODO: test if importing a features file onto an alignment which already
- // has features with links overwrites the original links.
-
- Hashtable featureLinks = new Hashtable();
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
- .getAlignment(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().getFeatureColours(), featureLinks,
- true, viewport.applet.getDefaultParameter("relaxedidmatch",
- false));
+ Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().getFeatureColours();
+ boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
+ "relaxedidmatch", false);
+ featuresFile = new FeaturesFile(file, paste).parse(
+ viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
if (featuresFile)
{
- if (featureLinks.size() > 0)
- {
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
- }
if (autoenabledisplay)
{
viewport.setShowSequenceFeatures(true);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
- FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+ FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
- e.getActionCommand(), viewport.getAlignment(),
+ fileFormat, viewport.getAlignment(),
viewport.getShowJVSuffix()));
}
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
+ FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = new FeaturesFile().printJalviewFormat(viewport
+ features = formatter.printJalviewFormat(viewport
.getAlignment().getSequencesArray(),
getDisplayedFeatureCols());
}
else
{
- features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+ features = formatter.printGffFormat(viewport.getAlignment()
.getSequencesArray(), getDisplayedFeatureCols());
}
}
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
viewport.setSelectionGroup(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (String ff : FileFormat.getWritableFormats())
{
-
- MenuItem item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ MenuItem item = new MenuItem(ff);
item.addActionListener(new java.awt.event.ActionListener()
{
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_thereshold"));
+ .getString("label.modify_identity_threshold"));
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
- .getString("label.modify_conservation_thereshold"));
+ .getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
}
// resolve data source
// TODO: this code should be a refactored to an io package
- String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
+ pdbFile, FileFormat.PDB);
if (protocol == null)
{
return false;
// make a note of the access mode and add
if (pdbentry.getProperty() == null)
{
- pdbentry.setProperty(new Hashtable());
+ pdbentry.setProperty(new Hashtable<String, String>());
}
- pdbentry.getProperty().put("protocol", protocol);
+ pdbentry.getProperty().put("protocol", protocol.toString());
toaddpdb.addPDBId(pdbentry);
alignPanel.getStructureSelectionManager()
.registerPDBEntry(pdbentry);
}
public void newStructureView(JalviewLite applet, PDBEntry pdb,
- SequenceI[] seqs, String[] chains, String protocol)
+ SequenceI[] seqs, String[] chains, DataSourceType protocol)
{
// Scrub any null sequences from the array
Object[] sqch = cleanSeqChainArrays(seqs, chains);
System.err
.println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
- if (protocol == null || protocol.trim().length() == 0
- || protocol.equals("null"))
+ if (protocol == null)
{
- protocol = (String) pdb.getProperty().get("protocol");
+ String sourceType = pdb.getProperty().get("protocol");
+ try
+ {
+ protocol = DataSourceType.valueOf(sourceType);
+ } catch (IllegalArgumentException e)
+ {
+ // ignore
+ }
if (protocol == null)
{
System.err.println("Couldn't work out protocol to open structure: "
{
// can only do alignments with Jmol
// find the last jmol window assigned to this alignment
- jalview.appletgui.AppletJmol ajm = null, tajm;
- Vector jmols = applet
- .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ AppletJmol ajm = null, tajm;
+ Vector jmols = applet.getAppletWindow(AppletJmol.class);
for (int i = 0, iSize = jmols.size(); i < iSize; i++)
{
- tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ tajm = (AppletJmol) jmols.elementAt(i);
if (tajm.ap.alignFrame == this)
{
ajm = tajm;
// otherwise, create a new window
if (applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ new AppletJmol(pdb, seqs, chains, alignPanel,
protocol);
applet.lastFrameX += 40;
applet.lastFrameY += 40;
git://source.jalview.org / jalview.git / blobdiff