*/
package jalview.javascript;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
+import jalview.api.JalviewApp;
import jalview.api.SequenceRenderer;
import jalview.appletgui.AlignFrame;
-import jalview.bin.JalviewLite;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolCommands;
import jalview.structure.AtomSpec;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
import java.util.ArrayList;
import java.util.List;
* @author Jim Procter (jprocter)
*
*/
-public class MouseOverStructureListener extends JSFunctionExec implements
- JsCallBack, StructureListener
+public class MouseOverStructureListener extends JSFunctionExec
+ implements JsCallBack, StructureListener
{
String _listenerfn;
- String[] modelSet;
+ public String[] modelSet;
- public MouseOverStructureListener(JalviewLite jalviewLite,
- String listener, String[] modelList)
+ public MouseOverStructureListener(JalviewApp app, String listener,
+ String[] modelList, boolean debug)
{
- super(jalviewLite);
+ super(app, debug);
_listenerfn = listener;
modelSet = modelList;
if (modelSet != null)
{
for (int i = 0; i < modelSet.length; i++)
{
- // ? leave file names 'as is' to match StructureMapping.pdbfile
- // modelSet[i] = resolveModelFile(modelSet[i]);
+ modelSet[i] = resolveModelFile(modelSet[i]);
}
}
}
/**
- * Returns the first out of file, file prefixed by document base, or file
+ * Returns the first out of: file, file prefixed by document base, or file
* prefixed by codebase which can be resolved to a valid URL. If none can,
* returns the input parameter value.
*
*/
public String resolveModelFile(String file)
{
- if (isValidUrl(file))
+ // TODO reuse JalviewLite.LoadingThread.addProtocol instead
+ if (HttpUtils.isValidUrl(file))
{
return file;
}
String db = jvlite.getDocumentBase().toString();
db = db.substring(0, db.lastIndexOf("/"));
String docBaseFile = db + "/" + file;
- if (isValidUrl(docBaseFile))
+ if (HttpUtils.isValidUrl(docBaseFile))
{
return docBaseFile;
}
String cb = jvlite.getCodeBase() + file;
- if (isValidUrl(cb))
+ if (HttpUtils.isValidUrl(cb))
{
return cb;
}
return file;
}
- /**
- * Returns true if it is possible to open an input stream at the given URL,
- * else false. The input stream is closed.
- *
- * @param file
- * @return
- */
- private boolean isValidUrl(String file)
- {
- InputStream is = null;
- try
- {
- is = new URL(file).openStream();
- if (is != null)
- {
- return true;
- }
- } catch (IOException x)
- {
- // MalformedURLException, FileNotFoundException
- return false;
- } finally
- {
- if (is != null)
- {
- try
- {
- is.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- return false;
- }
-
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return modelSet;
}
// JBPComment: yep - this is right! the Javascript harness uses the
// absolute pdbFile URI to locate the PDB file in the external viewer
executeJavascriptFunction(_listenerfn,
- new String[] { "mouseover", "" + atom.getPdbFile(),
- "" + atom.getChain(), "" + (atom.getPdbResNum()),
- "" + atom.getAtomIndex() });
+ new String[]
+ { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
+ "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
} catch (Exception ex)
{
System.err.println("Couldn't execute callback with " + _listenerfn
}
@Override
- public synchronized void updateColours(Object srce)
+ public synchronized void updateColours(Object source)
{
- final Object source = srce;
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(jvlite);
+ .getStructureSelectionManager(
+ jvlite.getStructureSelectionManagerProvider());
- if (JalviewLite.debug)
+ if (debug)
{
- System.err.println(this.getClass().getName() + " modelSet[0]: "
- + modelSet[0]);
+ System.err.println(
+ this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
ssm.reportMapping();
}
- if (source instanceof jalview.api.AlignmentViewPanel)
+ if (source instanceof AlignmentViewPanel)
{
+ AlignmentViewPanel panel = (AlignmentViewPanel) source;
SequenceI[][] sequence = new SequenceI[modelSet.length][];
for (int m = 0; m < modelSet.length; m++)
{
// }
}
- SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
- .getSequenceRenderer();
- FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
- .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
- ((jalview.appletgui.AlignmentPanel) source).av) : null;
+ SequenceRenderer sr = panel.getSequenceRenderer();
+ AlignViewportI vp = panel.getAlignViewport();
+ jalview.renderer.seqfeatures.FeatureRenderer fr = vp
+ .isShowSequenceFeatures() ? jvlite.getNewFeatureRenderer(vp)
+ : null;
if (fr != null)
{
- ((jalview.appletgui.FeatureRenderer) fr)
- .transferSettings(((jalview.appletgui.AlignmentPanel) source)
- .getFeatureRenderer());
+ fr.transferSettings(panel.getFeatureRenderer());
}
- ;
// Form a colour command from the given alignment panel for each distinct
// structure
- ArrayList<String[]> ccomands = new ArrayList<String[]>();
- ArrayList<String> pdbfn = new ArrayList<String>();
+ ArrayList<String[]> ccomands = new ArrayList<>();
+ ArrayList<String> pdbfn = new ArrayList<>();
StructureMappingcommandSet[] colcommands = JmolCommands
- .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
- ((AlignmentViewPanel) source).getAlignment());
+ .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
+ (AlignmentViewPanel) source);
if (colcommands == null)
{
return;
pdbfn.add(ccset.mapping);
}
- String mclass, mhandle;
String ccomandset[] = new String[sz];
sz = 0;
for (String[] ccset : ccomands)
System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
sz += ccset.length;
}
- if (jvlite.isJsMessageSetChanged(
- mclass = "colourstruct",
- mhandle = ((jalview.appletgui.AlignmentPanel) source).av
- .getViewId(), ccomandset))
+ String mclass = "colourstruct";
+ String mhandle = vp.getViewId();
+ if (isJsMessageSetChanged(mclass, mhandle, ccomandset, jvlite))
{
- jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
+ setJsMessageSet(mclass, mhandle, ccomandset, jvlite);
// and notify javascript handler
- String st[] = new String[] {
- "colourstruct",
- "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
- "" + ccomandset.length,
- jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
- .size()])) };
- try
- {
- executeJavascriptFunction(true, _listenerfn, st);
- } catch (Exception ex)
- {
- System.err.println("Couldn't execute callback with "
- + _listenerfn + " using args { " + st[0] + ", " + st[1]
- + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
- ex.printStackTrace();
-
- }
+ String st[] = new String[] { mclass, mhandle,
+ "" + ccomandset.length, jvlite.arrayToSeparatorList(
+ pdbfn.toArray(new String[pdbfn.size()])) };
+ executeJavascriptFunction(true, st);
}
/*
* new Thread(new Runnable() { public void run() { // and send to
*/
}
+ jvlite.updateColoursFromMouseOver(source, this);
}
@Override
return _listenerfn;
}
- public void finalise()
- {
- jvlite = null;
- super.finalize();
- }
-
@Override
public void releaseReferences(Object svl)
{
return true;
}
+ public void executeJavascriptFunction(boolean b, String[] st)
+ {
+ try
+ {
+ executeJavascriptFunction(true, _listenerfn, st);
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't execute callback with " + _listenerfn
+ + " using args { " + st[0] + ", " + st[1] + ", " + st[2] + ","
+ + st[3] + "}"); // + ","+st[4]+"\n");
+ ex.printStackTrace();
+
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff