import java.awt.*;
import java.awt.event.*;
+import java.util.*;
import jalview.appletgui.*;
import jalview.datamodel.*;
///////////////////////////////////////////
//The following public methods maybe called
//externally, eg via javascript in HTML page
-
+ /**
+ * @return list of selected sequences separated by "¬"
+ */
public String getSelectedSequences()
{
+ return getSelectedSequencesFrom(getDefaultTargetFrame());
+ }
+ public String getSelectedSequencesFrom(AlignFrame alf)
+ {
StringBuffer result = new StringBuffer("");
- if (initialAlignFrame.viewport.getSelectionGroup() != null)
+ if (alf.viewport.getSelectionGroup() != null)
{
- SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
+ SequenceI[] seqs = alf.viewport.getSelectionGroup().
getSequencesInOrder(
- initialAlignFrame.viewport.getAlignment());
+ alf.viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
return result.toString();
}
-
+
public String getAlignment(String format)
{
- return getAlignment(format, "true");
+ return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
+ }
+ public String getAlignmentFrom(AlignFrame alf, String format)
+ {
+ return getAlignmentFrom(alf, format, "true");
}
-
public String getAlignment(String format, String suffix)
{
+ return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
+ }
+ public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
+ {
try
{
boolean seqlimits = suffix.equalsIgnoreCase("true");
String reply = new AppletFormatAdapter().formatSequences(format,
- currentAlignFrame.viewport.getAlignment(), seqlimits);
+ alf.viewport.getAlignment(), seqlimits);
return reply;
}
catch (Exception ex)
public void loadAnnotation(String annotation)
{
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);
+ }
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
if (new AnnotationFile().readAnnotationFile(
- currentAlignFrame.getAlignViewport().getAlignment(), annotation,
+ alf.getAlignViewport().getAlignment(), annotation,
AppletFormatAdapter.PASTE))
{
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
}
else
{
- currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
}
}
public String getFeatures(String format)
{
- return currentAlignFrame.outputFeatures(false, format);
+ return getFeaturesFrom(getDefaultTargetFrame(), format);
+ }
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ return alf.outputFeatures(false, format);
}
-
public String getAnnotation()
{
- return currentAlignFrame.outputAnnotations(false);
+ return getAnnotationFrom(getDefaultTargetFrame());
+ }
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ return alf.outputAnnotations(false);
+ }
+ public AlignFrame newView()
+ {
+ return newViewFrom(getDefaultTargetFrame());
+ }
+ public AlignFrame newView(String name)
+ {
+ return newViewFrom(getDefaultTargetFrame(), name);
}
- public void loadAlignment(String text, String title)
+ public AlignFrame newViewFrom(AlignFrame alf)
+ {
+ return alf.newView(null);
+ }
+ public AlignFrame newViewFrom(AlignFrame alf, String name)
+ {
+ return alf.newView(name);
+ }
+ /**
+ *
+ * @param text alignment file as a string
+ * @param title window title
+ * @return null or new alignment frame
+ */
+ public AlignFrame loadAlignment(String text, String title)
{
Alignment al = null;
String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
format);
if (al.getHeight() > 0)
{
- new AlignFrame(al, this, title, false);
+ return new AlignFrame(al, this, title, false);
}
}
catch (java.io.IOException ex)
{
ex.printStackTrace();
}
+ return null;
}
////////////////////////////////////////////////
String file = "No file";
Button launcher = new Button("Start Jalview");
- //The currentAlignFrame is static, it will change
- //if and when the user selects a new window
+ /**
+ * The currentAlignFrame is static, it will change
+ * if and when the user selects a new window.
+ * Note that it will *never* point back to the embedded AlignFrame
+ * if the applet is started as embedded on the page and then afterwards a new view is created.
+ */
public static AlignFrame currentAlignFrame;
- //This is the first frame to be displayed, and does not change
+ /**
+ * This is the first frame to be displayed, and does not change.
+ * API calls will default to this instance if currentAlignFrame is null.
+ */
AlignFrame initialAlignFrame;
boolean embedded = false;
public boolean jmolAvailable = false;
+ public static boolean debug;
/**
* init method for Jalview Applet
*/
public void init()
{
- try
+ String dbg = getParameter("debug");
+ if (dbg!=null)
{
- Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter",
- true, Thread.currentThread().getContextClassLoader());
-
- jmolAvailable = true;
+ debug = dbg.toLowerCase().equals("true");
}
- catch (java.lang.ClassNotFoundException ex)
+ /**
+ * get the separator parameter if present
+ */
+ String sep = getParameter("separator");
+ if (sep!=null)
{
- System.out.println("Jmol not found - Using MCview for structures");
+ if (sep.length()>0)
+ { separator = sep;
+ if (debug)
+ {
+ System.err.println("Separator set to '"+separator+"'");
+ }
+ } else {
+ throw new Error("Invalid separator parameter - must be non-zero length");
+ }
}
-
int r = 255;
int g = 255;
int b = 255;
}
}
+ LoadJmolThread jmolAvailable = new LoadJmolThread();
+ jmolAvailable.start();
+
final JalviewLite applet = this;
if (getParameter("embedded") != null
&& getParameter("embedded").equalsIgnoreCase("true"))
}
}
- public static void main(String[] args)
- {
- if (args.length != 1)
- {
- System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
- System.exit(1);
- }
-
- String format = new jalview.io.IdentifyFile().Identify(args[0],
- AppletFormatAdapter.FILE);
-
- Alignment al = null;
- try
- {
- al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE,
- format);
- }
- catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
- if ( (al != null) && (al.getHeight() > 0))
- {
- AlignFrame af = new AlignFrame(al, null, args[0], false);
- af.statusBar.setText("Successfully loaded file " + args[0]);
- }
- }
/**
* Initialises and displays a new java.awt.Frame
}
lastFrameX -= 40;
lastFrameY -= 40;
+ if (frame instanceof EmbmenuFrame)
+ {
+ ((EmbmenuFrame) frame).destroyMenus();
+ }
frame.setMenuBar(null);
frame.dispose();
}
-
+
public void windowActivated(WindowEvent e)
{
if (frame instanceof AlignFrame)
{
currentAlignFrame = (AlignFrame) frame;
+ if (debug)
+ {
+ System.err.println("Activated window "+frame);
+ }
}
+ // be good.
+ super.windowActivated(e);
}
-
+ /* Probably not necessary to do this - see TODO above.
+ * (non-Javadoc)
+ * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
+ *
+ public void windowDeactivated(WindowEvent e)
+ {
+ if (currentAlignFrame == frame)
+ {
+ currentAlignFrame = null;
+ if (debug)
+ {
+ System.err.println("Deactivated window "+frame);
+ }
+ }
+ super.windowDeactivated(e);
+ }
+ */
});
frame.setVisible(true);
}
g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
g.drawString("Loading Data...", 50, this.getSize().height / 2);
}
+ }
+
+ class LoadJmolThread extends Thread
+ {
+ public void run()
+ {
+ try
+ {
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+ jmolAvailable = true;
+ }
+ }
+ catch (java.lang.ClassNotFoundException ex)
+ {
+ System.out.println("Jmol not available - Using MCview for structures");
+ }
+ }
}
+
class LoadingThread
extends Thread
{
public LoadingThread(String _file,
JalviewLite _applet)
{
+ if (applet.debug)
+ {
+ System.err.println("Loading thread started with:\n>>file\n"+_file+">>endfile");
+ }
file = _file;
if (file.startsWith("PASTE"))
{
file = addProtocol(file);
protocol = AppletFormatAdapter.URL;
}
+ if (applet.debug)
+ {
+ System.err.println("Protocol identified as '"+protocol+"'");
+ }
format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ if (applet.debug)
+ {
+ System.err.println("File identified as '"+format+"'");
+ }
applet = _applet;
}
public void run()
{
+ startLoading();
+ }
+
+ private void startLoading()
+ {
Alignment al = null;
try
{
}
if ( (al != null) && (al.getHeight() > 0))
{
- currentAlignFrame = new AlignFrame(al,
+ initialAlignFrame = new AlignFrame(al,
applet,
file,
embedded);
+ // update the focus.
+ currentAlignFrame = initialAlignFrame;
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
}
- initialAlignFrame = currentAlignFrame;
-
currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
String treeFile = applet.getParameter("tree");
}
}
+ /*
+ <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B PDB|1GAQ|1GAQ|C">
- param = getParameter("PDBFILE");
- if (param != null)
- {
+ <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- PDBEntry pdb = new PDBEntry();
+ <param name="PDBfile3" value="1q0o Q45135_9MICO">
+ */
- if (!inArchive(param) || jmolAvailable)
+
+ int pdbFileCount = 0;
+ do{
+ if (pdbFileCount > 0)
+ param = getParameter("PDBFILE" + pdbFileCount);
+ else
+ param = getParameter("PDBFILE");
+
+ if (param != null)
{
- param = addProtocol(param);
- }
+ PDBEntry pdb = new PDBEntry();
- pdb.setFile(param);
+ String seqstring;
+ SequenceI[] seqs = null;
+ String [] chains = null;
- String sequence = applet.getParameter("PDBSEQ");
+ StringTokenizer st = new StringTokenizer(param, " ");
- if (sequence != null)
- {
- if (jmolAvailable)
- new jalview.appletgui.AppletJmol(pdb,
- new SequenceI[]
- { (Sequence) currentAlignFrame.
- getAlignViewport().getAlignment().
- findName(sequence)},
- currentAlignFrame.alignPanel,
- protocol);
+ if (st.countTokens() < 2)
+ {
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
+ seqs = new SequenceI[]
+ {
+ (Sequence) currentAlignFrame.
+ getAlignViewport().getAlignment().
+ findName(sequence)};
+
+ }
+ else
+ {
+ param = st.nextToken();
+ Vector tmp = new Vector();
+ Vector tmp2 = new Vector();
+
+ while (st.hasMoreTokens())
+ {
+ seqstring = st.nextToken();
+ StringTokenizer st2 = new StringTokenizer(seqstring,"=");
+ if(st2.countTokens()>1)
+ {
+ //This is the chain
+ tmp2.addElement(st2.nextToken());
+ seqstring = st2.nextToken();
+ }
+ tmp.addElement( (Sequence) currentAlignFrame.
+ getAlignViewport().getAlignment().
+ findName(seqstring));
+ }
+
+ seqs = new SequenceI[tmp.size()];
+ tmp.copyInto(seqs);
+ if(tmp2.size()==tmp.size())
+ {
+ chains = new String[tmp2.size()];
+ tmp2.copyInto(chains);
+ }
+ }
+
+ if (inArchive(param) && !jmolAvailable)
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ }
else
+ {
+ protocol = AppletFormatAdapter.URL;
+ param = addProtocol(param);
+ }
+
+ pdb.setFile(param);
- new MCview.AppletPDBViewer(pdb,
- new SequenceI[]
- { (Sequence) currentAlignFrame.
- getAlignViewport().getAlignment().
- findName(sequence)},
- currentAlignFrame.alignPanel,
- protocol);
+ if(seqs!=null)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ ( (Sequence) seqs[i]).addPDBId(pdb);
+ }
+
+ if (jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(pdb,
+ seqs,
+ chains,
+ currentAlignFrame.alignPanel,
+ protocol);
+ lastFrameX += 40;
+ lastFrameY+=40;
+ }
+ else
+ new MCview.AppletPDBViewer(pdb,
+ seqs,
+ chains,
+ currentAlignFrame.alignPanel,
+ protocol);
+ }
}
+ pdbFileCount++;
+ }
+ while(pdbFileCount < 10);
+
+ /////////////////////////////
+ // modify display of features
+ //
+ // hide specific groups
+ param = getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupState(param, false);
+ }
+ // show specific groups
+ param = getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupState(param, true);
}
}
else
return file;
}
}
+ /**
+ * @return the default alignFrame acted on by the public applet methods.
+ * May return null with an error message on System.err indicating the fact.
+ */
+ protected AlignFrame getDefaultTargetFrame()
+ {
+ if (currentAlignFrame!=null)
+ {
+ return currentAlignFrame;
+ }
+ if (initialAlignFrame!=null)
+ {
+ return initialAlignFrame;
+ }
+ System.err.println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ return null;
+ }
+ /**
+ * separator used for separatorList
+ */
+ protected String separator = "|"; // this is a safe(ish) separator - tabs don't work for firefox
+ /**
+ * parse the string into a list
+ * @param list
+ * @return elements separated by separator
+ */
+ public String[] separatorListToArray(String list)
+ {
+ int seplen = separator.length();
+ if (list==null || list.equals(""))
+ return null;
+ java.util.Vector jv = new Vector();
+ int cp=0,pos;
+ while ((pos=list.indexOf(separator,cp))>cp)
+ {
+ jv.addElement(list.substring(cp,pos));
+ cp = pos+seplen;
+ }
+ if (cp<list.length())
+ {
+ jv.addElement(list.substring(cp));
+ }
+ if (jv.size()>0)
+ { String[] v = new String[jv.size()];
+ for (int i=0; i<v.length; i++)
+ {
+ v[i] = (String) jv.elementAt(i);
+ }
+ jv.removeAllElements();
+ if (debug)
+ {
+ System.err.println("Array from '"+separator+"' separated List:\n"+v.length);
+ for (int i=0; i<v.length;i++)
+ {
+ System.err.println("item "+i+" '"+v[i]+"'");
+ }
+ }
+ return v;
+ }
+ if (debug)
+ {
+ System.err.println("Empty Array from '"+separator+"' separated List");
+ }
+ return null;
+ }
+ /**
+ * concatenate the list with separator
+ * @param list
+ * @return concatenated string
+ */
+ public String arrayToSeparatorList(String[] list)
+ {
+ StringBuffer v = new StringBuffer();
+ if (list!=null)
+ {
+ for (int i=0,iSize=list.length-1;i<iSize;i++)
+ {
+ if (list[i]!=null)
+ {
+ v.append(list[i]);
+ }
+ v.append(separator);
+ }
+ if (list[list.length-1]!=null)
+ { v.append(list[list.length-1]);
+ }
+ if (debug)
+ {
+ System.err.println("Returning '"+separator+"' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (debug)
+ {
+ System.err.println("Returning empty '"+separator+"' separated List\n");
+ }
+ return "";
+ }
+ /**
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ */
+ public String getFeatureGroups()
+ {
+ String lst = arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroups());
+ return lst;
+ }
+ /**
+ * @param alf alignframe to get feature groups on
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ */
+ public String getFeatureGroupsOn(AlignFrame alf)
+ {
+ String lst = arrayToSeparatorList(alf.getFeatureGroups());
+ return lst;
+ }
+ /**
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ */
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroupsOfState(visible));
+ }
+ /**
+ * @param alf align frame to get groups of state visible
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ */
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ {
+ return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ } /**
+ * @param groups tab separated list of group names
+ * @param state true or false
+ * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
+ */
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state)
+ {
+ boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
+ alf.setFeatureGroupState(separatorListToArray(groups), st);
+ }
+ public void setFeatureGroupState(String groups, boolean state)
+ {
+ setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
+ }
+ /**
+ * List separator string
+ * @return the separator
+ */
+ public String getSeparator()
+ {
+ return separator;
+ }
+ /**
+ * List separator string
+ * @param separator the separator to set
+ */
+ public void setSeparator(String separator)
+ {
+ this.separator = separator;
+ }
}
git://source.jalview.org / jalview.git / blobdiff