import jalview.appletgui.FeatureSettings;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
// The following public methods maybe called
// externally, eg via javascript in HTML page
/**
- * @return String list of selected sequence IDs, each terminated by the 'boolean not' character (""+0x00AC) or
- * (¬)
+ * @return String list of selected sequence IDs, each terminated by the
+ * 'boolean not' character (""+0x00AC) or (¬)
*/
public String getSelectedSequences()
{
/**
* @param sep
* separator string or null for default
- * @return String list of selected sequence IDs, each terminated by given separator string
+ * @return String list of selected sequence IDs, each terminated by given
+ * separator string
*/
public String getSelectedSequences(String sep)
{
/**
* @param alf
* alignframe containing selection
- * @return String list of selected sequence IDs, each terminated by current default separator sequence
+ * @return String list of selected sequence IDs, each terminated by current
+ * default separator sequence
*
*/
public String getSelectedSequencesFrom(AlignFrame alf)
{
- return getSelectedSequencesFrom(alf,separator); // ""+0x00AC);
+ return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
/**
public void highlight(String sequenceId, String position,
String alignedPosition)
{
- highlightIn(getDefaultTargetFrame(), sequenceId, position, alignedPosition);
+ highlightIn(getDefaultTargetFrame(), sequenceId, position,
+ alignedPosition);
}
/**
* false, blank or something else - indicate if position is an
* alignment column or unaligned sequence position
*/
- public void highlightIn(AlignFrame alf, String sequenceId, String position,
- String alignedPosition)
+ public void highlightIn(AlignFrame alf, String sequenceId,
+ String position, String alignedPosition)
{
// TODO: could try to highlight in all alignments if alf==null
- SequenceI sq = alf.getAlignViewport().getAlignment()
- .findName(sequenceId);
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ SequenceI sq = matcher.findIdMatch(sequenceId);
if (sq != null)
{
int pos, apos = -1;
if (sep == null || sep.length() == 0)
{
sep = separator;
- } else {
+ }
+ else
+ {
if (debug)
{
- System.err.println("Selecting region using separator string '"+separator+"'");
+ System.err.println("Selecting region using separator string '"
+ + separator + "'");
}
}
// deparse fields
SequenceGroup sel = new SequenceGroup();
ColumnSelection csel = new ColumnSelection();
AlignmentI al = alf.viewport.getAlignment();
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
+ boolean seqsfound = true;
if (ids != null && ids.length > 0)
{
+ seqsfound = false;
for (int i = 0; i < ids.length; i++)
{
if (ids[i].trim().length() == 0)
{
continue;
}
- SequenceI sq = al.findName(ids[i]);
+ SequenceI sq = matcher.findIdMatch(ids[i]);
if (sq != null)
{
+ seqsfound = true;
sel.addSequence(sq, false);
}
}
}
+ boolean inseqpos = false;
if (cols != null && cols.length > 0)
{
boolean seset = false;
r--;
} catch (NumberFormatException ex)
{
- System.err
- .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
- + cl + "'");
- return;
+ if (cl.toLowerCase().equals("sequence"))
+ {
+ // we are in the dataset sequence's coordinate frame.
+ inseqpos = true;
+ }
+ else
+ {
+ System.err
+ .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
+ + cl + "'");
+ return;
+ }
}
if (r >= 0 && r <= alw)
{
}
}
}
- sel.setStartRes(start);
- sel.setEndRes(end);
- alf.select(sel, csel);
-
+ if (seqsfound)
+ {
+ // we only propagate the selection when it was the null selection, or the
+ // given sequences were found in the alignment.
+ if (inseqpos && sel.getSize() > 0)
+ {
+ // assume first sequence provides reference frame ?
+ SequenceI rs = sel.getSequenceAt(0);
+ start = rs.findIndex(start);
+ end = rs.findIndex(end);
+ if (csel != null)
+ {
+ Vector cs = csel.getSelected();
+ csel.clear();
+ for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)
+ {
+ csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))
+ .intValue()));
+ }
+ }
+ }
+ sel.setStartRes(start);
+ sel.setEndRes(end);
+ alf.select(sel, csel);
+ }
}
/**
*/
public String getSelectedSequencesAsAlignment(String format, String suffix)
{
- return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), format,
- suffix);
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
+ format, suffix);
}
/**
return "";
}
+ public String getAlignmentOrder()
+ {
+ return getAlignmentOrderFrom(getDefaultTargetFrame());
+ }
+
+ public String getAlignmentOrderFrom(AlignFrame alf)
+ {
+ return getAlignmentOrderFrom(alf, separator);
+ }
+
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ {
+ AlignmentI alorder = alf.getAlignViewport().getAlignment();
+ String[] order = new String[alorder.getHeight()];
+ for (int i = 0; i < order.length; i++)
+ {
+ order[i] = alorder.getSequenceAt(i).getName();
+ }
+ return arrayToSeparatorList(order);
+ }
+
+ public String orderBy(String order, String undoName)
+ {
+ return orderBy(order, undoName, separator);
+ }
+
+ public String orderBy(String order, String undoName, String sep)
+ {
+ return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
+ }
+
+ public String orderAlignmentBy(AlignFrame alf, String order,
+ String undoName, String sep)
+ {
+ String[] ids = separatorListToArray(order, sep);
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
+ {
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ int s = 0;
+ sqs = new SequenceI[ids.length];
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ sqs[s++] = sq;
+ }
+ }
+ if (s > 0)
+ {
+ SequenceI[] sqq = new SequenceI[s];
+ System.arraycopy(sqs, 0, sqq, 0, s);
+ sqs = sqq;
+ }
+ else
+ {
+ sqs = null;
+ }
+ }
+ if (sqs == null)
+ {
+ return "";
+ }
+ ;
+ AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+ if (undoName != null && undoName.trim().length() == 0)
+ {
+ undoName = null;
+ }
+
+ return alf.sortBy(aorder, undoName) ? "true" : "";
+ }
+
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector mouseoverListeners = new Vector();
+ private Vector javascriptListeners = new Vector();
public void setMouseoverListener(AlignFrame af, String listener)
{
}
jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
this, af, listener);
- mouseoverListeners.addElement(mol);
+ javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager()
.addStructureViewerListener(mol);
if (debug)
System.err.println("Added a mouseover listener for "
+ ((af == null) ? "All frames" : "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- System.err.println("There are now " + mouseoverListeners.size()
+ System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
}
jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
this, af, listener);
- mouseoverListeners.addElement(mol);
+ javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager()
.addSelectionListener(mol);
if (debug)
System.err.println("Added a selection listener for "
+ ((af == null) ? "All frames" : "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- System.err.println("There are now " + mouseoverListeners.size()
+ System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
+ public void setStructureListener(String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ return;
+ }
+ }
+ jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(this, listener);
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager()
+ .addStructureViewerListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a javascript structure viewer listener '"+listener+"'");
+ System.err.println("There are now " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
/**
* remove any callback using the given listener function and associated with
* the given alignFrame (or null for all callbacks)
}
}
boolean rprt = false;
- for (int ms = 0, msSize = mouseoverListeners.size(); ms < msSize;)
+ for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
{
- Object lstn = mouseoverListeners.elementAt(ms);
+ Object lstn = javascriptListeners.elementAt(ms);
JsCallBack lstner = (JsCallBack) lstn;
if ((af == null || lstner.getAlignFrame() == af)
&& (listener == null || lstner.getListenerFunction().equals(
listener)))
{
- mouseoverListeners.removeElement(lstner);
+ javascriptListeners.removeElement(lstner);
msSize--;
if (lstner instanceof SelectionListener)
{
}
if (rprt)
{
- System.err.println("There are now " + mouseoverListeners.size()
+ System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
}
public void stop()
{
- if (mouseoverListeners != null)
+ if (javascriptListeners != null)
{
- while (mouseoverListeners.size() > 0)
+ while (javascriptListeners.size() > 0)
{
- Object mol = mouseoverListeners.elementAt(0);
- mouseoverListeners.removeElement(mol);
+ Object mol = javascriptListeners.elementAt(0);
+ javascriptListeners.removeElement(mol);
if (mol instanceof SelectionListener)
{
StructureSelectionManager.getStructureSelectionManager()
* @param chain
* @param pdbfile
*/
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ public void mouseOverStructure(String pdbResNum, String chain, String pdbfile)
{
+ try {
StructureSelectionManager.getStructureSelectionManager()
- .mouseOverStructure(pdbResNum, chain, pdbfile);
+ .mouseOverStructure(new Integer(pdbResNum).intValue(), chain, pdbfile);
+ if (debug)
+ {
+ System.err.println("mouseOver for '"+pdbResNum+"' in chain '"+chain+"' in structure '"+pdbfile+"'");
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Ignoring invalid residue number string '"+pdbResNum+"'");
+ }
}
// //////////////////////////////////////////////
private boolean alignPdbStructures = false;
+ /**
+ * use an external structure viewer exclusively (no jmols or MCViews will be opened by JalviewLite itself)
+ */
+ public boolean useXtrnalSviewer=false;
+
public static boolean debug = false;
static String builddate = null, version = null;
// remove any handlers that might be hanging around from an earlier instance
try
{
- if (getAppletContext() instanceof sun.plugin.javascript.JSContext) {
- if (debug)
- {
- System.err.println("Applet context implements JSContext - should have callback support!");
- }
+ if (debug)
+ {
+ System.err.println("Applet context is '"
+ + getAppletContext().getClass().toString() + "'");
}
- JSObject scriptObject = JSObject.getWindow(this);
+ JSObject scriptObject = JSObject.getWindow(this);
+ if (debug && scriptObject != null)
+ {
+ System.err.println("Applet has Javascript callback support.");
+ }
+
} catch (Exception ex)
{
System.err
- .println("Warning: No JalviewLite javascript callbacks available.");
+ .println("Warning: No JalviewLite javascript callbacks available.");
if (debug)
{
ex.printStackTrace();
System.err.println("Build Date : " + getBuildDate());
}
+ String externalsviewer = getParameter("externalstructureviewer");
+ if (externalsviewer!=null)
+ {
+ useXtrnalSviewer=externalsviewer.trim().toLowerCase().equals("true");
+ }
/**
* if true disable the check for jmol
*/
}
setBackground(new Color(r, g, b));
-
+
file = getParameter("file");
if (file == null)
else if (file != null)
{
if (getParameter("showbutton") == null
- || !getParameter("showbutton").equalsIgnoreCase(
- "false"))
+ || !getParameter("showbutton").equalsIgnoreCase("false"))
{
// Add the JalviewLite 'Button' to the page
add(launcher);
initjscallback = initjscallback.trim();
if (initjscallback.length() > 0)
{
- JSObject scriptObject = null;
- try {
+ JSObject scriptObject = null;
+ try
+ {
scriptObject = JSObject.getWindow(this);
- } catch (Exception ex) {};
+ } catch (Exception ex)
+ {
+ }
+ ;
if (scriptObject != null)
{
try
{
// do onInit with the JS executor thread
new JSFunctionExec(this).executeJavascriptFunction(true,
- initjscallback, null, "Calling oninit callback '" + initjscallback
- + "'.");
+ initjscallback, null, "Calling oninit callback '"
+ + initjscallback + "'.");
} catch (Exception e)
{
System.err.println("Exception when executing _oninit callback '"
g.drawString("Loading Data...", 50, getSize().height / 2);
}
}
+
/**
* get all components associated with the applet of the given type
*
// Accumulate pdbs here if they are heading for the same view (if
// alignPdbStructures is true)
Vector pdbs = new Vector();
+ // create a lazy matcher if we're asked to
+ jalview.analysis.SequenceIdMatcher matcher = (applet.getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+ newAlignFrame.getAlignViewport().getAlignment().getSequencesArray()) : null;
+
do
{
if (pdbFileCount > 0)
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
seqs = new SequenceI[]
- { (Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(sequence) };
+ { matcher==null ? (Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(sequence) : matcher.findIdMatch(sequence) };
}
else
tmp2.addElement(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.addElement((Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(seqstring));
+ tmp.addElement(matcher==null ? (Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(seqstring) : matcher.findIdMatch(seqstring));
}
seqs = new SequenceI[tmp.size()];
/**
* separator used for separatorList
*/
- protected String separator = ""+((char)0x00AC); // the default used to be '|' but many sequence IDS include pipes.
-
+ protected String separator = "" + ((char) 0x00AC); // the default used to be
+ // '|' but many sequence
+ // IDS include pipes.
+
/**
* parse the string into a list
*
*/
public void setSeparator(String separator)
{
- if (separator==null || separator.length()<1)
+ if (separator == null || separator.length() < 1)
{
// reset to default
- separator = ""+((char)0x00AC);
+ separator = "" + ((char) 0x00AC);
}
this.separator = separator;
if (debug)
{
- System.err.println("Default Separator now: '"+separator+"'");
+ System.err.println("Default Separator now: '" + separator + "'");
}
}
git://source.jalview.org / jalview.git / blobdiff