import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
-import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
public void setGUINucleotide(boolean nucleotide)
{
showTranslation.setVisible(nucleotide);
+ showReverse.setVisible(nucleotide);
+ showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
+ @Override
public void setMenusForViewport()
{
setMenusFromViewport(viewport);
int startPos = aligmentStartEnd[0];
int endPos = aligmentStartEnd[1];
- int[] lowestRange = new int[2];
- int[] higestRange = new int[2];
+ int[] lowestRange = new int[] { -1, -1 };
+ int[] higestRange = new int[] { -1, -1 };
for (int[] hiddenCol : hiddenCols)
{
- // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
}
- // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
- // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
- if (lowestRange[0] == 0 && lowestRange[1] == 0)
+ if (lowestRange[0] == -1 && lowestRange[1] == -1)
{
startPos = aligmentStartEnd[0];
}
startPos = lowestRange[1] + 1;
}
- if (higestRange[0] == 0 && higestRange[1] == 0)
+ if (higestRange[0] == -1 && higestRange[1] == -1)
{
endPos = aligmentStartEnd[1];
}
else
{
- endPos = higestRange[0];
+ endPos = higestRange[0] - 1;
}
- // System.out.println("Export range : " + minPos + " - " + maxPos);
+ // System.out.println("Export range : " + startPos + " - " + endPos);
return new int[] { startPos, endPos };
}
public static void main(String[] args)
{
ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
- hiddenCols.add(new int[] { 0, 4 });
+ hiddenCols.add(new int[] { 0, 0 });
hiddenCols.add(new int[] { 6, 9 });
hiddenCols.add(new int[] { 11, 12 });
hiddenCols.add(new int[] { 33, 33 });
- hiddenCols.add(new int[] { 45, 50 });
+ hiddenCols.add(new int[] { 50, 50 });
int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
// System.out.println("Export range : " + x[0] + " - " + x[1]);
alignPanel.makeEPS(f);
}
+ @Override
public void createSVG(File f)
{
alignPanel.makeSVG(f);
}
}
+ @Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
return;
}
- format = new IdentifyFile().Identify(str, "Paste");
+ format = new IdentifyFile().identify(str, "Paste");
} catch (OutOfMemoryError er)
{
*/
if (sg.getSize() == viewport.getAlignment().getHeight())
{
- int confirm = JOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
-
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
{
- return;
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
}
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
-
SequenceI[] cut = sg.getSequences()
.toArray(new SequenceI[sg.getSize()]);
* @param cs
* DOCUMENT ME!
*/
+ @Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
+ if (cs instanceof TCoffeeColourScheme)
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ }
}
viewport.setGlobalColourScheme(cs);
// TODO 1: no mappings are set up for EMBL product
// TODO 2: if they were, should add them to protein alignment, not
// dna
- Set<AlignedCodonFrame> cf = prods.getCodonFrames();
+ List<AlignedCodonFrame> cf = prods.getCodonFrames();
for (AlignedCodonFrame acf : cf)
{
al.addCodonFrame(acf);
String type = null;
try
{
- type = new IdentifyFile().Identify(file, protocol);
+ type = new IdentifyFile().identify(file, protocol);
} catch (Exception ex)
{
type = null;
/**
* Attempt to load a "dropped" file or URL string: First by testing whether
- * it's and Annotation file, then a JNet file, and finally a features file. If
+ * it's an Annotation file, then a JNet file, and finally a features file. If
* all are false then the user may have dropped an alignment file onto this
* AlignFrame.
*
{
if (protocol == null)
{
- protocol = jalview.io.FormatAdapter.checkProtocol(file);
+ protocol = FormatAdapter.checkProtocol(file);
}
// if the file isn't identified, or not positively identified as some
// other filetype (PFAM is default unidentified alignment file type) then
// try to parse it as a features file
if (format == null)
{
- format = new IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
if (format.equalsIgnoreCase("JnetFile"))
{
viewport.setColumnSelection(cs);
isAnnotation = true;
}
- else
+ else if (IdentifyFile.FeaturesFile.equals(format))
{
- /*
- * if (format.equalsIgnoreCase("PDB")) {
- *
- * String pdbfn = ""; // try to match up filename with sequence id
- * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
- * new File(file); pdbfn = fl.getName(); } else if (protocol ==
- * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
- * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
- * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
- * // attempt to find a match in the alignment SequenceI mtch =
- * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
- * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
- * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
- * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
- * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
- * { System.err.println("Associated file : " + file + " with " +
- * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
- * TODO: maybe need to load as normal otherwise return; } }
- */
- // try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
+ if (parseFeaturesFile(file, protocol))
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ alignPanel.paintAlignment(true);
}
+ }
else
{
- alignPanel.paintAlignment(true);
+ new FileLoader().LoadFile(viewport, file, protocol, format);
}
- }
}
}
if (isAnnotation)
} catch (Exception x)
{
}
- ;
new OOMWarning(
"loading data "
+ (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
viewport.firePropertyChange("alignment", null, al);
}
+ @Override
public void setShowSeqFeatures(boolean b)
{
showSeqFeatures.setSelected(b);
{
// TODO no longer a menu action - refactor as required
final AlignmentI alignment = getViewport().getAlignment();
- Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
if (mappings == null)
{
return;
sf.setComplementVisible(this, show);
}
}
+
+ /**
+ * Generate the reverse (optionally complemented) of the selected sequences,
+ * and add them to the alignment
+ */
+ @Override
+ protected void showReverse_actionPerformed(boolean complement)
+ {
+ AlignmentI al = null;
+ try
+ {
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+ al = dna.reverseCdna(complement);
+ viewport.addAlignment(al, "");
+ } catch (Exception ex)
+ {
+ System.err.println(ex.getMessage());
+ return;
+ }
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff