*/
package jalview.bin;
+import java.util.Locale;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.StructureSelectionManagerProvider;
import jalview.appletgui.AlignFrame;
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;
int apos = -1;
try
{
- apos = new Integer(position).intValue();
+ apos = Integer.valueOf(position).intValue();
apos--;
} catch (NumberFormatException ex)
{
final StructureSelectionManagerProvider me = this;
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
- if (alignedPosition != null && (alignedPosition.trim().length() == 0
- || alignedPosition.toLowerCase().indexOf("false") > -1))
+ if (alignedPosition != null
+ && (alignedPosition.trim().length() == 0 || alignedPosition
+ .toLowerCase(Locale.ROOT).indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
{
if (debug)
{
- System.err.println("Selecting region using separator string '"
- + separator + "'");
+ jalview.bin.Console
+ .errPrintln("Selecting region using separator string '"
+ + separator + "'");
}
}
// deparse fields
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)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"ERROR: Couldn't parse first integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
try
{
- to = new Integer(cl.substring(p + 1)).intValue();
+ to = Integer.valueOf(cl.substring(p + 1)).intValue();
to--;
} catch (NumberFormatException ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"ERROR: Couldn't parse second integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
if (debug)
{
- System.err.println("Range '" + cl + "' deparsed as [" + from
- + "," + to + "]");
+ jalview.bin.Console.errPrintln("Range '" + cl
+ + "' deparsed as [" + from + "," + to + "]");
}
}
else
{
- System.err.println("ERROR: Invalid Range '" + cl
+ jalview.bin.Console.errPrintln("ERROR: Invalid Range '" + cl
+ "' deparsed as [" + from + "," + to + "]");
}
}
int r = -1;
try
{
- r = new Integer(cl).intValue();
+ r = Integer.valueOf(cl).intValue();
r--;
} catch (NumberFormatException ex)
{
- if (cl.toLowerCase().equals("sequence"))
+ if (cl.toLowerCase(Locale.ROOT).equals("sequence"))
{
// we are in the dataset sequence's coordinate frame.
inseqpos = true;
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"ERROR: Couldn't parse integer from point selection element of column selection string '"
+ cl + "'");
return;
csel.addElement(r);
if (debug)
{
- System.err.println("Point selection '" + cl
+ jalview.bin.Console.errPrintln("Point selection '" + cl
+ "' deparsed as [" + r + "]");
}
}
else
{
- System.err.println("ERROR: Invalid Point selection '" + cl
- + "' deparsed as [" + r + "]");
+ jalview.bin.Console
+ .errPrintln("ERROR: Invalid Point selection '" + cl
+ + "' deparsed as [" + r + "]");
}
}
}
SequenceI rs = sel.getSequenceAt(0);
start = rs.findIndex(start);
end = rs.findIndex(end);
- List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
+ List<Integer> cs = new ArrayList<>(csel.getSelected());
csel.clear();
for (Integer selectedCol : cs)
{
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<>();
/*
* (non-Javadoc)
listener = listener.trim();
if (listener.length() == 0)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"jalview Javascript error: Ignoring empty function for mouseover listener.");
return;
}
.addStructureViewerListener(mol);
if (debug)
{
- System.err.println("Added a mouseover listener for "
+ jalview.bin.Console.errPrintln("Added a mouseover listener for "
+ ((af == null) ? "All frames"
: "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- System.err.println("There are now " + javascriptListeners.size()
- + " listeners in total.");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
listener = listener.trim();
if (listener.length() == 0)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
.addSelectionListener(mol);
if (debug)
{
- System.err.println("Added a selection listener for "
+ jalview.bin.Console.errPrintln("Added a selection listener for "
+ ((af == null) ? "All frames"
: "Just views for "
+ af.getAlignViewport().getSequenceSetId()));
- System.err.println("There are now " + javascriptListeners.size()
- + " listeners in total.");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
listener = listener.trim();
if (listener.length() == 0)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
.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.");
+ jalview.bin.Console
+ .errPrintln("Added a javascript structure viewer listener '"
+ + listener + "'");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
rprt = debug;
if (debug)
{
- System.err.println("Removed listener '" + listener + "'");
+ jalview.bin.Console
+ .errPrintln("Removed listener '" + listener + "'");
}
}
else
}
if (rprt)
{
- System.err.println("There are now " + javascriptListeners.size()
- + " listeners in total.");
+ jalview.bin.Console.errPrintln("There are now "
+ + javascriptListeners.size() + " listeners in total.");
}
}
@Override
public void stop()
{
- System.err.println("Applet " + getName() + " stop().");
+ jalview.bin.Console.errPrintln("Applet " + getName() + " stop().");
tidyUp();
}
@Override
public void destroy()
{
- System.err.println("Applet " + getName() + " destroy().");
+ jalview.bin.Console.errPrintln("Applet " + getName() + " destroy().");
tidyUp();
}
try
{
StructureSelectionManager.getStructureSelectionManager(me)
- .mouseOverStructure(new Integer(pdbResNum).intValue(),
+ .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
chain, pdbfile);
if (debug)
{
}
} catch (NumberFormatException e)
{
- System.err.println("Ignoring invalid residue number string '"
- + pdbResNum + "'");
+ jalview.bin.Console
+ .errPrintln("Ignoring invalid residue number string '"
+ + pdbResNum + "'");
}
}
{
try
{
- alf.scrollTo(new Integer(topRow).intValue(),
- new Integer(leftHandColumn).intValue());
+ alf.scrollTo(Integer.valueOf(topRow).intValue(),
+ Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
- System.err.println("Couldn't parse integer arguments (topRow='"
- + topRow + "' and leftHandColumn='" + leftHandColumn
- + "')");
+ jalview.bin.Console
+ .errPrintln("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='"
+ + leftHandColumn + "')");
ex.printStackTrace();
}
}
{
try
{
- alf.scrollToRow(new Integer(topRow).intValue());
+ alf.scrollToRow(Integer.valueOf(topRow).intValue());
} catch (Exception ex)
{
- System.err.println("Couldn't parse integer arguments (topRow='"
- + topRow + "')");
+ jalview.bin.Console
+ .errPrintln("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
ex.printStackTrace();
}
{
try
{
- alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+ alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Couldn't parse integer arguments (leftHandColumn='"
+ leftHandColumn + "')");
ex.printStackTrace();
private boolean alignPdbStructures = false;
/**
- * use an external structure viewer exclusively (no jmols or MCViews will be
+ * use an external structure viewer exclusively (no jmols or mc_views will be
* opened by JalviewLite itself)
*/
public boolean useXtrnalSviewer = false;
{
if (debug)
{
- System.err.println("Applet context is '"
+ jalview.bin.Console.errPrintln("Applet context is '"
+ getAppletContext().getClass().toString() + "'");
}
JSObject scriptObject = JSObject.getWindow(this);
if (debug && scriptObject != null)
{
- System.err.println("Applet has Javascript callback support.");
+ jalview.bin.Console
+ .errPrintln("Applet has Javascript callback support.");
}
} catch (Exception ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning: No JalviewLite javascript callbacks available.");
if (debug)
{
if (debug)
{
- System.err.println("JalviewLite Version " + getVersion());
- System.err.println("Build Date : " + getBuildDate());
- System.err.println("Installation : " + getInstallation());
+ jalview.bin.Console.errPrintln("JalviewLite Version " + getVersion());
+ jalview.bin.Console.errPrintln("Build Date : " + getBuildDate());
+ jalview.bin.Console.errPrintln("Installation : " + getInstallation());
}
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
- useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT)
+ .equals(TRUE);
}
/**
* if true disable the check for jmol
separator = sep;
if (debug)
{
- System.err.println("Separator set to '" + separator + "'");
+ jalview.bin.Console
+ .errPrintln("Separator set to '" + separator + "'");
}
}
else
{
if (tries > 0)
{
- System.err.println("LiveConnect request thread going to sleep.");
+ jalview.bin.Console
+ .errPrintln("LiveConnect request thread going to sleep.");
}
try
{
;
if (tries++ > 0)
{
- System.err.println("LiveConnect request thread woken up.");
+ jalview.bin.Console
+ .errPrintln("LiveConnect request thread woken up.");
}
try
{
}
} catch (Exception jsex)
{
- System.err.println("Attempt " + tries
+ jalview.bin.Console.errPrintln("Attempt " + tries
+ " to access LiveConnect javascript failed.");
}
}
"Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
{
- System.err.println("Exception when executing _oninit callback '"
- + initjscallback + "'.");
+ jalview.bin.Console
+ .errPrintln("Exception when executing _oninit callback '"
+ + initjscallback + "'.");
e.printStackTrace();
}
}
else
{
- System.err.println("Not executing _oninit callback '"
+ jalview.bin.Console.errPrintln("Not executing _oninit callback '"
+ initjscallback + "' - no scripting allowed.");
}
}
((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
if (debug)
{
- System.err.println("Activated window " + frame);
+ jalview.bin.Console.errPrintln("Activated window " + frame);
}
}
// be good.
*
* public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
* frame) { currentAlignFrame = null; if (debug) {
- * System.err.println("Deactivated window "+frame); } }
+ * jalview.bin.Console.errPrintln("Deactivated window "+frame); } }
* super.windowDeactivated(e); }
*/
});
}
if (!jmolAvailable)
{
- System.out.println(
- "Jmol not available - Using MCview for structures");
+ jalview.bin.Console.outPrintln(
+ "Jmol not available - Using mc_view for structures");
}
} catch (java.lang.ClassNotFoundException ex)
{
jmolAvailable = false;
if (debug)
{
- System.err.println(
- "Skipping Jmol check. Will use MCView (probably)");
+ jalview.bin.Console.errPrintln(
+ "Skipping Jmol check. Will use mc_view (probably)");
}
}
checkedForJmol = true;
{
if (JalviewLite.debug)
{
- System.err.println(msg);
+ jalview.bin.Console.errPrintln(msg);
}
}
{
if (debug)
{
- System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + withDocBase + "'");
+ jalview.bin.Console.errPrintln("Prepended document base '"
+ + documentBase + "' to make: '" + withDocBase + "'");
}
protocol = DataSourceType.URL;
return withDocBase;
protocol = DataSourceType.URL;
if (debug)
{
- System.err.println("Prepended codebase '" + codeBase
+ jalview.bin.Console.errPrintln("Prepended codebase '" + codeBase
+ "' to make: '" + withCodeBase + "'");
}
return withCodeBase;
+ " as "
+ (al1.isNucleotide() ? "protein product" : "cDNA")
+ " for " + af.getTitle();
- System.err.println(msg);
+ jalview.bin.Console.errPrintln(msg);
}
}
dbgMsg(">>>Dump finished.");
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exception when trying to dump the content of the file parameter.");
e.printStackTrace();
}
else
{
param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
- List<String> tmp2 = new ArrayList<String>();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> tmp2 = new ArrayList<>();
while (st.hasMoreTokens())
{
{
// this may not really be a problem but we give a warning
// anyway
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ i + ")");
}
JnetAnnotationMaker.add_annotation(predictions,
alignFrame.viewport.getAlignment(), 0, false);
// false == do not add sequence profile from concise output
- SequenceI repseq = alignFrame.viewport.getAlignment()
- .getSequenceAt(0);
- alignFrame.viewport.getAlignment().setSeqrep(repseq);
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq);
- alignFrame.viewport.getAlignment().setHiddenColumns(cs);
+
+ alignFrame.viewport.getAlignment().setupJPredAlignment();
+
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
result = true;
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Annotations were not added from annotation file '"
+ param + "'");
}
{
if (debug)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Attempting to load T-COFFEE score file from the scoreFile parameter");
}
result = alignFrame.loadScoreFile(sScoreFile);
if (!result)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to parse T-COFFEE parameter as a valid score file ('"
+ sScoreFile + "')");
}
boolean rtn = (getClass().getResourceAsStream("/" + f) != null);
if (debug)
{
- System.err.println("Resource '" + f + "' was "
+ jalview.bin.Console.errPrintln("Resource '" + f + "' was "
+ (rtn ? "" : "not ") + "located by classloader.");
}
return rtn;
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + f + " " + ex);
+ jalview.bin.Console.outPrintln(
+ "Exception checking resources: " + f + " " + ex);
return false;
}
}
{
return initialAlignFrame;
}
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
return null;
}
jv.removeAllElements();
if (debug)
{
- System.err.println("Array from '" + separator
+ jalview.bin.Console.errPrintln("Array from '" + separator
+ "' separated List:\n" + v.length);
for (int i = 0; i < v.length; i++)
{
- System.err.println("item " + i + " '" + v[i] + "'");
+ jalview.bin.Console.errPrintln("item " + i + " '" + v[i] + "'");
}
}
return v;
}
if (debug)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Empty Array from '" + separator + "' separated List");
}
return null;
{
System.err
.println("Returning '" + separator + "' separated List:\n");
- System.err.println(v);
+ jalview.bin.Console.errPrintln(v);
}
return v.toString();
}
if (debug)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Returning empty '" + separator + "' separated List\n");
}
return "" + separator;
final String groups, boolean state)
{
final boolean st = state;// !(state==null || state.equals("") ||
- // state.toLowerCase().equals("false"));
+ // state.toLowerCase(Locale.ROOT).equals("false"));
java.awt.EventQueue.invokeLater(new Runnable()
{
@Override
this.separator = separator;
if (debug)
{
- System.err.println("Default Separator now: '" + separator + "'");
+ jalview.bin.Console
+ .errPrintln("Default Separator now: '" + separator + "'");
}
}
// callInitCallback();
}
- private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
+ private Hashtable<String, long[]> jshashes = new Hashtable<>();
- private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
public void setJsMessageSet(String messageclass, String viewId,
String[] colcommands)
Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
if (msgset == null)
{
- msgset = new Hashtable<String, String[]>();
+ msgset = new Hashtable<>();
jsmessages.put(messageclass, msgset);
}
msgset.put(viewId, colcommands);
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- System.err.println("Couldn't parse '" + colprop + "' as a colour for "
- + colparam);
+ jalview.bin.Console.errPrintln("Couldn't parse '" + colprop
+ + "' as a colour for " + colparam);
}
return (col == null) ? defcolour : col;
}
}
if (debug)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"resolveUrlForLocalOrAbsolute returning " + resolvedPath);
}
return resolvedPath;
: getDocumentBase());
if (debug)
{
- System.err.println("Show url (prepended " + prepend
+ jalview.bin.Console.errPrintln("Show url (prepended " + prepend
+ " - toggle resolvetocodebase if code/docbase resolution is wrong): "
+ url);
}
{
if (debug)
{
- System.err.println("Show url: " + url);
+ jalview.bin.Console.errPrintln("Show url: " + url);
}
}
if (url.indexOf("javascript:") == 0)
git://source.jalview.org / jalview.git / blobdiff