* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
- * @param RNAannot
+ * @param rnaAnnotation
*/
- private void _updateRnaSecStr(CharSequence RNAannot)
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
{
try
{
- bps = Rna.getModeleBP(RNAannot);
- _rnasecstr = Rna.getBasePairs(bps);
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
{
return;
}
- Rna.HelixMap(_rnasecstr);
- // setRNAStruc(RNAannot);
if (_rnasecstr != null && _rnasecstr.length > 0)
{
*/
private Map<Integer, Annotation> sequenceMapping;
- /** DOCUMENT ME!! */
+ /**
+ * lower range for quantitative data
+ */
public float graphMin;
- /** DOCUMENT ME!! */
+ /**
+ * Upper range for quantitative data
+ */
public float graphMax;
/**
}
}
- // JBPNote: what does this do ?
- public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
- {
- bps = Rna.getModeleBP(RNAannot);
- }
-
/**
* Creates a new AlignmentAnnotation object.
*
firstChar = annotations[i].displayCharacter.charAt(0);
// check to see if it looks like a sequence or is secondary structure
// labelling.
- if (annotations[i].secondaryStructure != ' '
- && !hasIcons
- &&
- // Uncomment to only catch case where
- // displayCharacter==secondary
- // Structure
- // to correctly redisplay SS annotation imported from Stockholm,
- // exported to JalviewXML and read back in again.
- // &&
- // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
- firstChar != ' '
- && firstChar != '$'
- && firstChar != 0xCE
- && firstChar != '('
- && firstChar != '['
- && firstChar != '>'
- && firstChar != '{'
- && firstChar != 'A'
- && firstChar != 'B'
- && firstChar != 'C'
- && firstChar != 'D'
- && firstChar != 'E'
- && firstChar != 'F'
- && firstChar != 'G'
- && firstChar != 'H'
- && firstChar != 'I'
- && firstChar != 'J'
- && firstChar != 'K'
- && firstChar != 'L'
- && firstChar != 'M'
- && firstChar != 'N'
- && firstChar != 'O'
- && firstChar != 'P'
- && firstChar != 'Q'
- && firstChar != 'R'
- && firstChar != 'S'
- && firstChar != 'T'
- && firstChar != 'U'
- && firstChar != 'V'
- && firstChar != 'W'
- && firstChar != 'X'
- && firstChar != 'Y'
- && firstChar != 'Z'
+ if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
+ // Uncomment to only catch case where
+ // displayCharacter==secondary
+ // Structure
+ // to correctly redisplay SS annotation imported from Stockholm,
+ // exported to JalviewXML and read back in again.
+ // &&
+ // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+ firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
+ && firstChar != '(' && firstChar != '[' && firstChar != '>'
+ && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
+ && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
+ && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
+ && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
+ && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
+ && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
+ && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
+ && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
+ && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
{
return ((index + offset < 0) || (index + offset) >= max
|| annotations[index + offset] == null
- || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
- : annotations[index + offset].displayCharacter == null
- || annotations[index + offset].displayCharacter
- .length() == 0 ? annotations[index + offset].secondaryStructure
- : annotations[index + offset].displayCharacter
- .charAt(0));
+ || (annotations[index + offset].secondaryStructure <= ' ')
+ ? ' '
+ : annotations[index + offset].displayCharacter == null
+ || annotations[index
+ + offset].displayCharacter
+ .length() == 0
+ ? annotations[index
+ + offset].secondaryStructure
+ : annotations[index
+ + offset].displayCharacter
+ .charAt(0));
}
@Override
for (int i = offset; i < mx; i++)
{
- string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
- : (annotations[i].displayCharacter == null
- || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
- : annotations[i].displayCharacter.charAt(0));
+ string[i] = (annotations[i] == null
+ || (annotations[i].secondaryStructure <= 32))
+ ? ' '
+ : (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter
+ .length() == 0
+ ? annotations[i].secondaryStructure
+ : annotations[i].displayCharacter
+ .charAt(0));
}
return new String(string);
}
Annotation[] temp = new Annotation[endRes - startRes + 1];
if (startRes < annotations.length)
{
- System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
- + 1);
+ System.arraycopy(annotations, startRes, temp, 0,
+ endRes - startRes + 1);
}
if (sequenceRef != null)
{
@Override
public String toString()
{
+ if (annotations == null)
+ {
+ return "";
+ }
StringBuilder buffer = new StringBuilder(256);
for (int i = 0; i < annotations.length; i++)
* @param seqRef
* @param startRes
* @param alreadyMapped
+ * - annotation are at aligned columns
*/
public void createSequenceMapping(SequenceI seqRef, int startRes,
boolean alreadyMapped)
{
if (i + 1 < iSize)
{
- System.arraycopy(annotations, i + 1, annotations, i, iSize - i
- - 1);
+ System.arraycopy(annotations, i + 1, annotations, i,
+ iSize - i - 1);
}
iSize--;
}
{
if (sequenceRef != null)
{
- boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
- .getDatasetSequence() == null;
+ boolean rIsDs = sequenceRef.getDatasetSequence() == null,
+ tIsDs = sequenceI.getDatasetSequence() == null;
if (sequenceRef != sequenceI
- && (rIsDs && !tIsDs && sequenceRef != sequenceI
- .getDatasetSequence())
- && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI)
- && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI
- .getDatasetSequence())
+ && (rIsDs && !tIsDs
+ && sequenceRef != sequenceI.getDatasetSequence())
+ && (!rIsDs && tIsDs
+ && sequenceRef.getDatasetSequence() != sequenceI)
+ && (!rIsDs && !tIsDs
+ && sequenceRef.getDatasetSequence() != sequenceI
+ .getDatasetSequence())
&& !sequenceRef.equals(sequenceI))
{
// if sequenceRef isn't intersecting with sequenceI
* @param colSel
*/
public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- ColumnSelection colSel)
+ HiddenColumns hidden)
{
this(alignmentAnnotation);
if (annotations == null)
{
return;
}
- colSel.makeVisibleAnnotation(this);
+ hidden.makeVisibleAnnotation(this);
}
public void setPadGaps(boolean padgaps, char gapchar)
throw new Error(
"liftOver currently not implemented for transfer of annotation between different types of seqeunce");
}
- boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
- .getTo() == sq.getDatasetSequence()) : false;
+ boolean mapIsTo = (sp2sq != null)
+ ? (sp2sq.getTo() == sq
+ || sp2sq.getTo() == sq.getDatasetSequence())
+ : false;
// TODO build a better annotation element map and get rid of annotations[]
Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
{
for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
{
- Integer mpos = Integer.valueOf(mapIsTo ? sp2sq
- .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie
- .getKey()));
+ Integer mpos = Integer
+ .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
+ : sp2sq.getPosition(ie.getKey()));
if (mpos >= sq.getStart() && mpos <= sq.getEnd())
{
mapForsq.put(mpos, ie.getValue());
* up to and excluding the target column; if the count is less
* than 1, the opening bracket is unmatched, so return its match
*/
- String closer = String.valueOf(Rna
- .getMatchingClosingParenthesis(symbol));
+ String closer = String
+ .valueOf(Rna.getMatchingClosingParenthesis(symbol));
String opener = String.valueOf(symbol);
int count = 0;
for (int j = col + 1; j < column; j++)
{
return counter++;
}
+
+ /**
+ *
+ * @return true for rows that have a range of values in their annotation set
+ */
+ public boolean isQuantitative()
+ {
+ return graphMin < graphMax;
+ }
}
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
- import jalview.analysis.NJTree;
+ import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+ import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
- import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+ import jalview.renderer.ResidueShader;
+ import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+ import jalview.schemes.ResidueColourScheme;
import jalview.schemes.UserColourScheme;
- import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
+ import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Vector;
import javax.swing.JInternalFrame;
- import javax.swing.JOptionPane;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision: 1.141 $
*/
- public class AlignViewport extends AlignmentViewport implements
- SelectionSource, CommandListener
+ public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
{
Font font;
- NJTree currentTree = null;
+ TreeModel currentTree = null;
boolean cursorMode = false;
*/
public AlignViewport(AlignmentI al)
{
- setAlignment(al);
+ super(al);
init();
}
public AlignViewport(AlignmentI al, String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
init();
+
}
/**
* @param hiddenColumns
* ColumnSelection
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
{
- setAlignment(al);
+ super(al);
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
* @param seqsetid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid)
{
this(al, hiddenColumns, seqsetid, null);
* @param viewid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
+
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
- viewStyle.setShowUnconserved(Cache
- .getDefault("SHOW_UNCONSERVED", false));
+ viewStyle.setShowUnconserved(
+ Cache.getDefault("SHOW_UNCONSERVED", false));
sortByTree = Cache.getDefault("SORT_BY_TREE", false);
followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
- sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- Preferences.SORT_ANNOTATIONS,
- SequenceAnnotationOrder.NONE.name()));
- showAutocalculatedAbove = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
- viewStyle.setScaleProteinAsCdna(Cache.getDefault(
- Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
+ viewStyle.setScaleProteinAsCdna(
+ Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
}
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
-
+ if (Cache.getDefault("NORMALISE_GAPS", true))
+ {
+ alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(
+ 0));
+ }
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
if (hconsensus == null && !isDataset)
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ String colourProperty = alignment.isNucleotide()
+ ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
- String propertyValue = Cache.getProperty(colourProperty);
- if (propertyValue == null)
+ String schemeName = Cache.getProperty(colourProperty);
+ if (schemeName == null)
{
- // fall back on this property for backwards compatibility
- propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ // only DEFAULT_COLOUR available in Jalview before 2.9
+ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
}
- if (propertyValue != null)
- {
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
- propertyValue);
+ ColourSchemeI colourScheme = ColourSchemeProperty
+ .getColourScheme(alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- if (globalColourScheme instanceof UserColourScheme)
- {
- globalColourScheme = UserDefinedColours.loadDefaultColours();
- ((UserColourScheme) globalColourScheme).setThreshold(0,
- isIgnoreGapsConsensus());
- }
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
- }
- }
-
- /**
- * get the consensus sequence as displayed under the PID consensus annotation
- * row.
- *
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
- {
- if (consensus == null)
+ if (colourScheme instanceof UserColourScheme)
{
- updateConsensus(null);
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
}
- if (consensus == null)
+
+ if (residueShading != null)
{
- return null;
+ residueShading.setConsensus(hconsensus);
}
- StringBuffer seqs = new StringBuffer();
- for (int i = 0; i < consensus.annotations.length; i++)
- {
- if (consensus.annotations[i] != null)
- {
- if (consensus.annotations[i].description.charAt(0) == '[')
- {
- seqs.append(consensus.annotations[i].description.charAt(1));
- }
- else
- {
- seqs.append(consensus.annotations[i].displayCharacter);
- }
- }
- }
-
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "
- + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
- return sq;
}
boolean validCharWidth;
/**
- * update view settings with the given font. You may need to call
- * alignPanel.fontChanged to update the layout geometry
- *
- * @param setGrid
- * when true, charWidth/height is set according to font mentrics
+ * {@inheritDoc}
*/
+ @Override
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
- .getCharHeight();
if (setGrid)
{
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
-
}
/**
* @param tree
* DOCUMENT ME!
*/
- public void setCurrentTree(NJTree tree)
+ public void setCurrentTree(TreeModel tree)
{
currentTree = tree;
}
*
* @return DOCUMENT ME!
*/
- public NJTree getCurrentTree()
+ public TreeModel getCurrentTree()
{
return currentTree;
}
{
end = alignment.getWidth();
}
- viscontigs = colSel.getVisibleContigs(start, end);
+ viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
return viscontigs;
}
public void sendSelection()
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ .getStructureSelectionManager(Desktop.instance)
+ .sendSelection(new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()),
+ this);
}
/**
*/
public AlignmentPanel getAlignPanel()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(this.getSequenceSetId());
for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
&& pdb.getChainCode() != null)
{
if (pdbRefEntry.getChainCode().equalsIgnoreCase(
- pdb.getChainCode())
- && !choosenSeqs.contains(sq))
+ pdb.getChainCode()) && !choosenSeqs.contains(sq))
{
choosenSeqs.add(sq);
continue;
* <ul>
* <li>compute the equivalent edit on the mapped sequences</li>
* <li>apply the mapped edit</li>
- * <li>'apply' the source edit to the working copy of the source sequences</li>
+ * <li>'apply' the source edit to the working copy of the source
+ * sequences</li>
* </ul>
*
* @param command
}
}
- setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight());
firePropertyChange("alignment", null, getAlignment().getSequences());
}
*/
protected boolean openLinkedAlignment(AlignmentI al, String title)
{
- String[] options = new String[] {
- MessageManager.getString("action.no"),
+ String[] options = new String[] { MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[] { title }));
+ newAlignFrame.statusBar.setText(MessageManager
+ .formatMessage("label.successfully_loaded_file", new Object[]
+ { title }));
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
try
{
- newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(
+ jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
* is protein, the mappings to cDNA will be registered with
* StructureSelectionManager as a side-effect.
*/
- AlignFrame copyMe = new AlignFrame(complement,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
AlignmentI al = newAlignFrame.viewport.getAlignment();
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setDontScrollComplement(true);
+ complementPanel.setToScrollComplementPanel(false);
complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
}
}
protected void iprmsAdd_actionPerformed(ActionEvent e)
{
RestInputParamEditDialog dialog = new RestInputParamEditDialog(this,
- currentservice, "param"
- + (1 + currentservice.getInputParams().size()));
+ currentservice,
+ "param" + (1 + currentservice.getInputParams().size()));
if (dialog.wasUpdated())
{
currentservice.getInputParams().put(dialog.current.token,
MessageManager.getString("label.select_return_type"));
for (final JvDataType type : JvDataType.values())
{
- popup.add(new JMenuItem(type.name())).addActionListener(
- new ActionListener()
+ popup.add(new JMenuItem(type.name()))
+ .addActionListener(new ActionListener()
{
@Override
currentservice.addResultDatatype(JvDataType.ANNOTATION);
}
initGuiWith(currentservice);
- rdata.setSelectedIndex(p == -1 ? currentservice.getResultDataTypes()
- .size() - 1 : p + 1);
+ rdata.setSelectedIndex(
+ p == -1 ? currentservice.getResultDataTypes().size() - 1
+ : p + 1);
}
@Override
StringBuffer warnings = new StringBuffer();
for (String its : _iparam)
{
- Matcher mtch = Pattern.compile("(\\S+)\\s(\\S+):\\[(.+)]").matcher(
- its);
+ Matcher mtch = Pattern.compile("(\\S+)\\s(\\S+):\\[(.+)]")
+ .matcher(its);
if (mtch.find())
{
- if (!RestServiceDescription.parseTypeString(mtch.group(2) + ":"
- + mtch.group(3), mtch.group(1), mtch.group(2),
- mtch.group(3), inputTypes, warnings))
+ if (!RestServiceDescription.parseTypeString(
+ mtch.group(2) + ":" + mtch.group(3), mtch.group(1),
+ mtch.group(2), mtch.group(3), inputTypes, warnings))
{
- System.err
- .println("IMPLEMENTATION PROBLEM: Cannot parse RestService input parameter string '"
+ System.err.println(
+ "IMPLEMENTATION PROBLEM: Cannot parse RestService input parameter string '"
+ its + "'" + "\n" + warnings);
}
}
}
- char gc = gapChar.getSelectedItem() == null ? ' ' : ((String) gapChar
- .getSelectedItem()).charAt(0);
+ char gc = gapChar.getSelectedItem() == null ? ' '
+ : ((String) gapChar.getSelectedItem()).charAt(0);
RestServiceDescription newService = new RestServiceDescription(
- (String) action.getSelectedItem(), descr.getText().trim(), name
- .getText().trim(), url.getText().trim(), urlsuff
- .getText().trim(), inputTypes, hSeparable.isSelected(),
+ (String) action.getSelectedItem(), descr.getText().trim(),
+ name.getText().trim(), url.getText().trim(),
+ urlsuff.getText().trim(), inputTypes, hSeparable.isSelected(),
vSeparable.isSelected(), gc);
if (newService.isValid())
} catch (Throwable x)
{
- System.err
- .println("IMPLEMENTATION PROBLEM: Cannot parse RestService output parameter string '"
+ System.err.println(
+ "IMPLEMENTATION PROBLEM: Cannot parse RestService output parameter string '"
+ its + "'" + "\n" + warnings);
}
}
}
else
{
- System.err
- .println("IMPLEMENTATION PROBLEM: Restservice generated from GUI is invalid\n"
+ System.err.println(
+ "IMPLEMENTATION PROBLEM: Restservice generated from GUI is invalid\n"
+ warnings);
}
}
else
{
- parseRes.setText(MessageManager
- .formatMessage(
- "label.parsing_failed_syntax_errors_shown_below_param",
- new String[] { rsd.getInvalidMessage() }));
+ parseRes.setText(MessageManager.formatMessage(
+ "label.parsing_failed_syntax_errors_shown_below_param",
+ new String[]
+ { rsd.getInvalidMessage() }));
parseWarnings.setVisible(true);
}
} catch (Throwable e)
{
e.printStackTrace();
- parseRes.setText(MessageManager
- .formatMessage(
- "label.parsing_failed_unrecoverable_exception_thrown_param",
- new String[] { e.toString() }));
+ parseRes.setText(MessageManager.formatMessage(
+ "label.parsing_failed_unrecoverable_exception_thrown_param",
+ new String[]
+ { e.toString() }));
parseWarnings.setVisible(true);
}
}
final Thread runner = Thread.currentThread();
JFrame df = new JFrame();
df.getContentPane().setLayout(new BorderLayout());
- df.getContentPane().add((nulserv = !nulserv)
- ? new RestServiceEditorPane(jalview.ws.rest.RestClient
- .makeShmmrRestClient().getRestDescription())
- : new RestServiceEditorPane(), BorderLayout.CENTER);
+ df.getContentPane().add(
+ (nulserv = !nulserv) ? new RestServiceEditorPane(
+ jalview.ws.rest.clientdefs.ShmrRestClient
+ .makeShmmrRestClient()
+ .getRestDescription())
+ : new RestServiceEditorPane(),
+ BorderLayout.CENTER);
df.setBounds(100, 100, 600, 400);
df.addComponentListener(new ComponentListener()
{
}
};
- JPanel pane = new JPanel(new BorderLayout()), okcancel = new JPanel(
- new FlowLayout());
+ JPanel pane = new JPanel(new BorderLayout()),
+ okcancel = new JPanel(new FlowLayout());
pane.add(this, BorderLayout.CENTER);
okcancel.add(jvd.ok);
okcancel.add(jvd.cancel);
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+ import jalview.renderer.AnnotationRenderer;
+ import jalview.util.Comparison;
import java.awt.Color;
import java.util.IdentityHashMap;
public class AnnotationColourGradient extends FollowerColourScheme
{
+ /**
+ * map positional scores to transparency rather than colour
+ */
+ boolean positionToTransparency = true;
+
+ /**
+ * compute shade based on annotation row score
+ */
+ boolean perLineScore = true;
+
public static final int NO_THRESHOLD = -1;
public static final int BELOW_THRESHOLD = 0;
public static final int ABOVE_THRESHOLD = 1;
- public AlignmentAnnotation annotation;
+ private final AlignmentAnnotation annotation;
- int aboveAnnotationThreshold = -1;
+ private final int aboveAnnotationThreshold;
public boolean thresholdIsMinMax = false;
- GraphLine annotationThreshold;
+ private GraphLine annotationThreshold;
- float r1, g1, b1, rr, gg, bb;
+ private int redMin;
+
+ private int greenMin;
+
+ private int blueMin;
+
+ private int redRange;
+
+ private int greenRange;
+
+ private int blueRange;
private boolean predefinedColours = false;
*/
private boolean noGradient = false;
- IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+ private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
- colourScheme, aboveAnnotationThreshold);
+ getColourScheme(), aboveAnnotationThreshold);
acg.thresholdIsMinMax = thresholdIsMinMax;
acg.annotationThreshold = (annotationThreshold == null) ? null
: new GraphLine(annotationThreshold);
- acg.r1 = r1;
- acg.g1 = g1;
- acg.b1 = b1;
- acg.rr = rr;
- acg.gg = gg;
- acg.bb = bb;
+ acg.redMin = redMin;
+ acg.greenMin = greenMin;
+ acg.blueMin = blueMin;
+ acg.redRange = redRange;
+ acg.greenRange = greenRange;
+ acg.blueRange = blueRange;
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
acg.noGradient = noGradient;
+ acg.positionToTransparency = positionToTransparency;
+ acg.perLineScore = perLineScore;
return acg;
}
{
if (originalColour instanceof AnnotationColourGradient)
{
- colourScheme = ((AnnotationColourGradient) originalColour).colourScheme;
+ setColourScheme(((AnnotationColourGradient) originalColour)
+ .getColourScheme());
}
else
{
- colourScheme = originalColour;
+ setColourScheme(originalColour);
}
this.annotation = annotation;
annotationThreshold = annotation.threshold;
}
// clear values so we don't get weird black bands...
- r1 = 254;
- g1 = 254;
- b1 = 254;
- rr = 0;
- gg = 0;
- bb = 0;
+ redMin = 254;
+ greenMin = 254;
+ blueMin = 254;
+ redRange = 0;
+ greenRange = 0;
+ blueRange = 0;
noGradient = true;
checkLimits();
annotationThreshold = annotation.threshold;
}
- r1 = minColour.getRed();
- g1 = minColour.getGreen();
- b1 = minColour.getBlue();
+ redMin = minColour.getRed();
+ greenMin = minColour.getGreen();
+ blueMin = minColour.getBlue();
- rr = maxColour.getRed() - r1;
- gg = maxColour.getGreen() - g1;
- bb = maxColour.getBlue() - b1;
+ redRange = maxColour.getRed() - redMin;
+ greenRange = maxColour.getGreen() - greenMin;
+ blueRange = maxColour.getBlue() - blueMin;
noGradient = false;
checkLimits();
seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
}
// resolve the context containing all the annotation for the sequence
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+ ? alignment
: alignment.getContext();
- boolean f = true, rna = false;
- for (AlignmentAnnotation alan : alcontext
- .findAnnotation(annotation.getCalcId()))
+ boolean f = true, sf = true, rna = false;
+ long plcount = 0, ancount = 0;
+ for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
+ .getCalcId()))
{
if (alan.sequenceRef != null
- && (alan.label != null && annotation != null && alan.label
- .equals(annotation.label)))
+ && (alan.label != null && annotation != null
+ && alan.label.equals(annotation.label)))
{
+ ancount++;
if (!rna && alan.isRNA())
{
rna = true;
aamin = alan.graphMin;
}
f = false;
+ if (alan.score == alan.score)
+ {
+ if (sf || alan.score < plmin)
+ {
+ plmin = alan.score;
+ }
+ if (sf || alan.score > plmax)
+ {
+ plmax = alan.score;
+ }
+ sf = false;
+ plcount++;
+ }
}
}
+ if (plcount > 0 && plcount == ancount)
+ {
+ perLineScore = plcount == ancount;
+ aamax=plmax;
+ }
if (rna)
{
ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
}
}
- float aamin = 0f, aamax = 0f;
+ /**
+ * positional annotation max/min
+ */
+ double aamin = 0.0, aamax = 0.0;
+
+ /**
+ * per line score max/min
+ */
+ double plmin = Double.NaN, plmax = Double.NaN;
- public String getAnnotation()
+ public AlignmentAnnotation getAnnotation()
{
- return annotation.label;
+ return annotation;
}
public int getAboveThreshold()
public Color getMinColour()
{
- return new Color((int) r1, (int) g1, (int) b1);
+ return new Color(redMin, greenMin, blueMin);
}
public Color getMaxColour()
{
- return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+ return new Color(redMin + redRange, greenMin + greenRange,
+ blueMin + blueRange);
}
/**
}
/**
- * DOCUMENT ME!
+ * Returns the colour for a given character and position in a sequence
*
- * @param n
- * DOCUMENT ME!
+ * @param c
+ * the residue character
* @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * the aligned position
+ * @param seq
+ * the sequence
+ * @return
*/
@Override
public Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour = Color.white;
- AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
- .get(seq) : this.annotation);
- if (annotation == null)
+ /*
+ * locate the annotation we are configured to colour by
+ */
+ AlignmentAnnotation ann = (seqAssociated && seqannot != null
+ ? seqannot.get(seq)
+ : this.annotation);
+
+ /*
+ * if gap or no annotation at position, no colour (White)
+ */
+ if (ann == null || ann.annotations == null
+ || j >= ann.annotations.length || ann.annotations[j] == null
+ || Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+
+ Annotation aj = ann.annotations[j];
+ // 'use original colours' => colourScheme != null
+ // -> look up colour to be used
+ // predefined colours => preconfigured shading
+ // -> only use original colours reference if thresholding enabled &
+ // minmax exists
+ // annotation.hasIcons => null or black colours replaced with glyph
+ // colours
+ // -> reuse original colours if present
+ // -> if thresholding enabled then return colour on non-whitespace glyph
+
+ /*
+ * if threshold applies, and annotation fails the test - no colour (white)
+ */
+ if (annotationThreshold != null)
+ {
+ if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && aj.value < annotationThreshold.value)
+ || (aboveAnnotationThreshold == BELOW_THRESHOLD
+ && aj.value > annotationThreshold.value))
+ {
+ return Color.white;
+ }
+ }
+
+ /*
+ * If 'use original colours' then return the colour of the annotation
+ * at the aligned position - computed using the background colour scheme
+ */
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
{
- return currentColour;
+ return aj.colour;
}
- if ((threshold == 0) || aboveThreshold(c, j))
+
+ Color result = Color.white;
+ if (ann.hasIcons && ann.graph == AlignmentAnnotation.NO_GRAPH)
{
- if (annotation.annotations != null
- && j < annotation.annotations.length
- && annotation.annotations[j] != null
- && !jalview.util.Comparison.isGap(c))
+ /*
+ * secondary structure symbol colouring
+ */
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-')
{
- Annotation aj = annotation.annotations[j];
- // 'use original colours' => colourScheme != null
- // -> look up colour to be used
- // predefined colours => preconfigured shading
- // -> only use original colours reference if thresholding enabled &
- // minmax exists
- // annotation.hasIcons => null or black colours replaced with glyph
- // colours
- // -> reuse original colours if present
- // -> if thresholding enabled then return colour on non-whitespace glyph
-
- if (aboveAnnotationThreshold == NO_THRESHOLD
- || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
- : aj.value <= annotationThreshold.value)))
+ if (getColourScheme() != null)
{
- if (predefinedColours && aj.colour != null
- && !aj.colour.equals(Color.black))
- {
- currentColour = aj.colour;
- }
- else if (annotation.hasIcons
- && annotation.graph == AlignmentAnnotation.NO_GRAPH)
- {
- if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
- && aj.secondaryStructure != '-')
- {
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- else
- {
- if (annotation.isRNA())
- {
- currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
- }
- else
- {
- currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
- : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
- : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
- }
- }
- }
- else
- {
- //
- return Color.white;
- }
- }
- else if (noGradient)
+ result = getColourScheme().findColour(c, j, seq, null, 0f);
+ }
+ else
+ {
+ if (ann.isRNA())
{
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- else
- {
- if (aj.colour != null)
- {
- currentColour = aj.colour;
- }
- }
+ result = ColourSchemeProperty.rnaHelices[(int) aj.value];
}
else
{
- currentColour = shadeCalculation(annotation, j);
+ result = ann.annotations[j].secondaryStructure == 'H'
+ ? AnnotationRenderer.HELIX_COLOUR
+ : ann.annotations[j].secondaryStructure == 'E'
+ ? AnnotationRenderer.SHEET_COLOUR
+ : AnnotationRenderer.STEM_COLOUR;
}
}
- if (conservationColouring)
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+ else if (noGradient)
+ {
+ if (getColourScheme() != null)
+ {
+ result = getColourScheme().findColour(c, j, seq, null, 0f);
+ }
+ else
+ {
+ if (aj.colour != null)
{
- currentColour = applyConservation(currentColour, j);
+ result = aj.colour;
}
}
}
- return currentColour;
+ else
+ {
+ result = shadeCalculation(ann, j);
+ }
+
+ return result;
}
- private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ /**
+ * Returns a graduated colour for the annotation at the given column. If there
+ * is a threshold value, and it is used as the top/bottom of the colour range,
+ * and the value satisfies the threshold condition, then a colour
+ * proportionate to the range from the threshold is calculated. For all other
+ * cases, a colour proportionate to the annotation's min-max range is
+ * calulated. Note that thresholding is _not_ done here (a colour is computed
+ * even if threshold is not passed).
+ *
+ * @param ann
+ * @param col
+ * @return
+ */
+ Color shadeCalculation(AlignmentAnnotation ann, int col)
{
-
- // calculate a shade
float range = 1f;
- if (thresholdIsMinMax
- && annotation.threshold != null
+ float value = ann.annotations[col].value;
+ if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value >= annotation.threshold.value)
+ && value >= ann.threshold.value)
{
- range = (annotation.annotations[j].value - annotation.threshold.value)
- / (annotation.graphMax - annotation.threshold.value);
+ range = (value - ann.threshold.value)
+ / (ann.graphMax - ann.threshold.value);
}
- else if (thresholdIsMinMax && annotation.threshold != null
+ else if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value >= annotation.graphMin)
+ && value <= ann.threshold.value)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
+ range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
}
else
{
- if (annotation.graphMax != annotation.graphMin)
+ if (ann.graphMax != ann.graphMin)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.graphMax - annotation.graphMin);
+ range = (value - ann.graphMin) / (ann.graphMax - ann.graphMin);
}
else
{
range = 0f;
}
}
+
- int dr = (int) (redRange * range + redMin);
- int dg = (int) (greenRange * range + greenMin);
- int db = (int) (blueRange * range + blueMin);
-
- return new Color(dr, dg, db);
+ // midtr sets the ceiling for bleaching out the shading
+ int trans = 0, midtr = 239;
+ if (perLineScore)
+ {
+ trans = (int) ((1f - range) * midtr);
+ range = (float) ((annotation.score - plmin) / (plmax - aamin));
+ }
+ int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+ * range + b1);
+ if (annotation.score == annotation.score && positionToTransparency)
+ {
+ return new Color(Math.min(dr + trans, midtr), Math.min(dg
+ + trans, midtr), Math.min(db + trans, midtr));
+ }
+ else
+ {
+ return new Color(dr, dg, db);
+ }
}
public boolean isPredefinedColours()
{
seqAssociated = sassoc;
}
+
+ public boolean isThresholdIsMinMax()
+ {
+ return thresholdIsMinMax;
+ }
+
+ public void setThresholdIsMinMax(boolean minMax)
+ {
+ this.thresholdIsMinMax = minMax;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Annotation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
private static final int TO_UPPER_CASE = 'a' - 'A';
- private static final char GAP_SPACE = ' ';
+ public static final char GAP_SPACE = ' ';
- private static final char GAP_DOT = '.';
+ public static final char GAP_DOT = '.';
- private static final char GAP_DASH = '-';
+ public static final char GAP_DASH = '-';
- public static final String GapChars = new String(new char[] { GAP_SPACE,
- GAP_DOT, GAP_DASH });
+ public static final String GapChars = new String(
+ new char[]
+ { GAP_SPACE, GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
* int
* @return float
*/
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+ public static float compare(SequenceI ii, SequenceI jj, int start,
+ int end)
{
String si = ii.getSequenceAsString();
String sj = jj.getSequenceAsString();
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
* @param s2
* SequenceI
* @return float
+ * @deprecated use PIDModel.computePID()
*/
+ @Deprecated
public final static float PID(String seq1, String seq2)
{
return PID(seq1, seq2, 0, seq1.length());
static final int caseShift = 'a' - 'A';
// Another pid with region specification
- public final static float PID(String seq1, String seq2, int start, int end)
+ /**
+ * @deprecated use PIDModel.computePID()
+ */
+ @Deprecated
+ public final static float PID(String seq1, String seq2, int start,
+ int end)
{
return PID(seq1, seq2, start, end, true, false);
}
* @param ungappedOnly
* - if true - only count PID over ungapped columns
* @return
+ * @deprecated use PIDModel.computePID()
*/
+ @Deprecated
public final static float PID(String seq1, String seq2, int start,
int end, boolean wcGaps, boolean ungappedOnly)
{
*/
public static final boolean isGap(char c)
{
- return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
+ return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE);
}
/**
{
return false;
}
- char[][] letters = new char[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- char[] sequence = seqs[i].getSequence();
- if (sequence != null)
- {
- letters[i] = sequence;
- }
- }
- }
- return areNucleotide(letters);
- }
-
- /**
- * Answers true if more than 85% of the sequence residues (ignoring gaps) are
- * A, G, C, T or U, else false. This is just a heuristic guess and may give a
- * wrong answer (as AGCT are also amino acid codes).
- *
- * @param letters
- * @return
- */
- static final boolean areNucleotide(char[][] letters)
- {
int ntCount = 0;
int aaCount = 0;
- for (char[] seq : letters)
+ for (SequenceI seq : seqs)
{
if (seq == null)
{
}
// TODO could possibly make an informed guess just from the first sequence
// to save a lengthy calculation
- for (char c : seq)
+ int len = seq.getLength();
+ for (int i = 0; i < len; i++)
{
+ char c = seq.getCharAt(i);
if (isNucleotide(c))
{
ntCount++;
flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
- .size()]);
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
return isNucleotide(oneDArray);
}
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
-import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Hashtable;
import java.util.Vector;
import javax.swing.JMenu;
* @author JimP
*
*/
- public class RestClient extends WSClient implements WSClientI,
- WSMenuEntryProviderI
+ public class RestClient extends WSClient
+ implements WSClientI, WSMenuEntryProviderI
{
RestServiceDescription service;
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = MessageManager.formatMessage(
- "label.webservice_job_title", new String[] {
- service.details.Action, service.details.Name });
+ WebServiceJobTitle = MessageManager
+ .formatMessage("label.webservice_job_title", new String[]
+ { service.details.Action, service.details.Name });
WebServiceName = service.details.Name;
WebServiceReference = "No reference - go to url for more info";
if (service.details.description != null)
}
if (!headless)
{
- wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
- + WebServiceReference, true);
+ wsInfo = new WebserviceInfo(WebServiceJobTitle,
+ WebServiceName + "\n" + WebServiceReference, true);
wsInfo.setRenderAsHtml(true);
}
final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(MessageManager.formatMessage(
- "label.rest_client_submit", new String[] {
- service.details.Action, service.details.Name }));
+ submit.setToolTipText(MessageManager
+ .formatMessage("label.rest_client_submit", new String[]
+ { service.details.Action, service.details.Name }));
submit.addActionListener(new ActionListener()
{
{
// intersect groups with selected region
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true,
+ true);
viewTitle = MessageManager.formatMessage(
- "label.select_visible_region_of",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
else
{
// use selected region to partition alignment
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), false, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), false,
+ true);
}
viewTitle = MessageManager.formatMessage(
- "label.select_unselect_visible_regions_from",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_unselect_visible_regions_from", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
else
{
// just take selected region intersection
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true, true);
viewTitle = MessageManager.formatMessage(
- "label.select_visible_region_of",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
}
{
// standard alignment view without selection present
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), null, av.hasHiddenColumns(), false,
- true);
+ av.getAlignment().getHiddenColumns(), null,
+ av.hasHiddenColumns(), false, true);
viewTitle = ""
- + (av.hasHiddenColumns() ? (new StringBuffer(" ")
- .append(MessageManager
- .getString("label.visible_region_of"))
- .toString()) : "") + af.getTitle();
+ + (av.hasHiddenColumns()
+ ? (new StringBuffer(" ")
+ .append(MessageManager
+ .getString("label.visible_region_of"))
+ .toString())
+ : "")
+ + af.getTitle();
}
RestJobThread jobsthread = new RestJobThread(this);
else
{
// TODO: try to tell the user why the job couldn't be started.
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- (jobsthread.hasWarnings() ? jobsthread.getWarnings()
- : MessageManager
- .getString("label.job_couldnt_be_started_check_input")),
- MessageManager
- .getString("label.unable_start_web_service_analysis"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ (jobsthread.hasWarnings() ? jobsthread.getWarnings()
+ : MessageManager.getString(
+ "label.job_couldnt_be_started_check_input")),
+ MessageManager
+ .getString("label.unable_start_web_service_analysis"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
- public static RestClient makeShmmrRestClient()
- {
- String action = "Analysis",
- description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)",
- name = MessageManager.getString("label.multiharmony");
- Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
- jalview.ws.rest.params.JobConstant toolp;
- // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
- // iparams.put(toolp.token, toolp);
- // toolp = new
- // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
- // iparams.put(toolp.token, toolp);
-
- jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
- // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
- // so we always upload our files.
- aliinput.token = "ali_file";
- aliinput.writeAsFile = true;
- iparams.put(aliinput.token, aliinput);
- jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
- sgroups.setMinsize(2);
- sgroups.min = 2;// need at least two group defined to make a partition
- iparams.put("groups", sgroups);
- sgroups.token = "groups";
- sgroups.sep = " ";
- RestServiceDescription shmrService = new RestServiceDescription(action,
- description, name,
- "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview", // ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
- "?tool=jalview", iparams, true, false, '-');
- // a priori knowledge of the data returned from the service
- shmrService.addResultDatatype(JvDataType.ANNOTATION);
- return new RestClient(shmrService);
- }
-
public AlignmentPanel recoverAlignPanelForView()
{
AlignmentPanel[] aps = Desktop
try
{
for (RestServiceDescription descr : RestServiceDescription
- .parseDescriptions(
- jalview.bin.Cache.getDefault(RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ .parseDescriptions(jalview.bin.Cache.getDefault(
+ RSBS_SERVICES,
+ ShmrRestClient.makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
} catch (Exception ex)
{
- System.err
- .println("Serious - RSBS descriptions in user preferences are corrupt!");
+ System.err.println(
+ "Serious - RSBS descriptions in user preferences are corrupt!");
ex.printStackTrace();
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.Annotation;
- import jalview.datamodel.ColumnSelection;
+ import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import org.apache.http.entity.mime.HttpMultipartMode;
import org.apache.http.entity.mime.MultipartEntity;
import org.apache.http.impl.client.DefaultHttpClient;
-import org.apache.http.protocol.BasicHttpContext;
-import org.apache.http.protocol.HttpContext;
import org.apache.http.util.EntityUtils;
public class RestJobThread extends AWSThread
{
jobs = new RestJob[1];
jobs[0] = new RestJob(0, this,
- restClient._input.getVisibleAlignment(restClient.service
- .getGapCharacter()),
+ restClient._input.getVisibleAlignment(
+ restClient.service.getGapCharacter()),
restClient._input.getVisibleContigs());
// need a function to get a range on a view/alignment and return both
// annotation, groups and selection subsetted to just that region.
{
int[] viscontig = restClient._input.getVisibleContigs();
AlignmentI[] viscontigals = restClient._input
- .getVisibleContigAlignments(restClient.service
- .getGapCharacter());
+ .getVisibleContigAlignments(
+ restClient.service.getGapCharacter());
if (viscontigals != null && viscontigals.length > 0)
{
jobs = new RestJob[viscontigals.length];
protected void doHttpReq(Stage stg, RestJob rj, String postUrl)
throws Exception
{
- StringBuffer respText = new StringBuffer();
- // con.setContentHandlerFactory(new
- // jalview.ws.io.mime.HttpContentHandler());
HttpRequestBase request = null;
String messages = "";
if (stg == Stage.SUBMIT)
{
if (input.getValue().validFor(rj))
{
- postentity.addPart(input.getKey(), input.getValue()
- .formatForInput(rj));
+ postentity.addPart(input.getKey(),
+ input.getValue().formatForInput(rj));
}
else
{
{
DefaultHttpClient httpclient = new DefaultHttpClient();
- HttpContext localContext = new BasicHttpContext();
HttpResponse response = null;
try
{
Cache.log.debug("Processing result set.");
processResultSet(rj, response, request);
break;
+
case 202:
- rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
- + "<a href=" + rj.getJobId() + "\">" + rj.getJobId()
- + "</a><br>";
- rj.running = true;
+ markJobAsRunning(rj);
break;
+
+ case 201:
+ // Created - redirect may be present. Fallthrough to 302
case 302:
- Header[] loc;
- if (!rj.isSubmitted()
- && (loc = response
- .getHeaders(HTTPConstants.HEADER_LOCATION)) != null
- && loc.length > 0)
- {
- if (loc.length > 1)
- {
- Cache.log.warn("Ignoring additional " + (loc.length - 1)
- + " location(s) provided in response header ( next one is '"
- + loc[1].getValue() + "' )");
- }
- rj.setJobId(loc[0].getValue());
- rj.setSubmitted(true);
- }
+ extractJobId(rj, response);
completeStatus(rj, response);
break;
case 500:
- // Failed.
- rj.setSubmitted(true);
- rj.setAllowedServerExceptions(0);
- rj.setSubjobComplete(true);
- rj.error = true;
- rj.running = false;
- completeStatus(rj, response,
- "" + getStage(stg) + "failed. Reason below:\n");
+ markAsFailed(rj, response);
+ completeStatus(rj, response, "" + getStage(stg)
+ + "failed. Reason below:\n");
-
break;
default:
// Some other response. Probably need to pop up the content in a window.
rj.setSubmitted(true);
try
{
- completeStatus(
- rj,
- response,
- ""
- + getStage(stg)
- + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
- + request.getURI()
- + "\">"
- + request.getURI()
- + "</a><br/>Filtered response content below:<br/>");
+ completeStatus(rj, response, "" + getStage(stg)
+ + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
+ + request.getURI() + "\">" + request.getURI()
+ + "</a><br/>Filtered response content below:<br/>");
} catch (IOException e)
{
Cache.log.debug("IOException when consuming unhandled response",
}
}
+ private void markAsFailed(RestJob rj, HttpResponse response)
+ {
+ // Failed.
+ rj.setSubmitted(true);
+ rj.setAllowedServerExceptions(0);
+ rj.setSubjobComplete(true);
+ rj.error = true;
+ rj.running = false;
+ }
+
+ /**
+ * set the jobRunning flag and post a link to the physical result page encoded
+ * in rj.getJobId()
+ *
+ * @param rj
+ */
+ private void markJobAsRunning(RestJob rj)
+ {
+ rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
+ + "<a href="
+ + rj.getJobId()
+ + "\">"
+ + rj.getJobId()
+ + "</a><br>";
+ rj.running = true;
+ }
+
+ /**
+ * extract the job ID URL from the redirect page. Does nothing if job is
+ * already running.
+ *
+ * @param rj
+ * @param response
+ */
+ private void extractJobId(RestJob rj, HttpResponse response)
+ {
+ Header[] loc;
+ if (!rj.isSubmitted())
+ {
+
+ // redirect URL - typical for IBIVU type jobs.
+ if ((loc = response.getHeaders(HTTPConstants.HEADER_LOCATION)) != null
+ && loc.length > 0)
+ {
+ if (loc.length > 1)
+ {
+ Cache.log
+ .warn("Ignoring additional "
+ + (loc.length - 1)
+ + " location(s) provided in response header ( next one is '"
+ + loc[1].getValue() + "' )");
+ }
+ rj.setJobId(loc[0].getValue());
+ rj.setSubmitted(true);
+ }
+ }
+ }
+
/**
* job has completed. Something valid should be available from con
*
} catch (Error ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} catch (Exception ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} finally
{
rj.error = true;
rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
- + rj.resSet.getUrl()
- + "\">"
- + rj.resSet.getUrl()
+ + rj.resSet.getUrl() + "\">" + rj.resSet.getUrl()
+ "</a><br>";
}
}
// total number of distinct alignment sets generated by job set.
int numAlSets = 0, als = 0;
List<AlignmentI> destAls = new ArrayList<AlignmentI>();
- List<jalview.datamodel.ColumnSelection> destColsel = new ArrayList<jalview.datamodel.ColumnSelection>();
+ List<jalview.datamodel.HiddenColumns> destColsel = new ArrayList<jalview.datamodel.HiddenColumns>();
List<List<NewickFile>> trees = new ArrayList<List<NewickFile>>();
do
RestJob rj = (RestJob) jobs[nrj];
int contigs[] = input.getVisibleContigs();
AlignmentI destAl = null;
- jalview.datamodel.ColumnSelection destCs = null;
+ jalview.datamodel.HiddenColumns destHCs = null;
// Resolve destAl for this data.
if (als == 0 && rj.isInputContextModified())
{
if (!restClient.isAlignmentModified() && merge)
{
destAl = restClient.av.getAlignment();
- destCs = restClient.av.getColumnSelection();
- resultDest
- .add(restClient.isShowResultsInNewView() ? AddDataTo.newView
- : AddDataTo.currentView);
+ destHCs = restClient.av.getAlignment().getHiddenColumns();
+ resultDest.add(restClient.isShowResultsInNewView()
+ ? AddDataTo.newView
+ : AddDataTo.currentView);
destPanels.add(restClient.recoverAlignPanelForView());
}
else
newAlignment = true;
// recreate the input alignment data
Object[] idat = input
- .getAlignmentAndColumnSelection(gapCharacter);
+ .getAlignmentAndHiddenColumns(gapCharacter);
destAl = new Alignment((SequenceI[]) idat[0]);
- destCs = (ColumnSelection) idat[1];
+ destHCs = (HiddenColumns) idat[1];
resultDest.add(AddDataTo.newAlignment);
// but do not add to the alignment panel list - since we need to
// create a whole new alignFrame set.
}
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
}
}
else
{
// TODO: decide if multiple multiple alignments returned by
// non-vseparable services are allowed.
- Cache.log
- .warn("dealing with multiple alignment products returned by non-vertically separable service.");
+ Cache.log.warn(
+ "dealing with multiple alignment products returned by non-vertically separable service.");
}
// recover reference to last alignment created for this rest frame
// ready for extension
destAl = destAls.get(als);
- destCs = destColsel.get(als);
+ destHCs = destColsel.get(als);
}
else
{
newview = input.getUpdatedView(rseqs, orders, gapCharacter);
}
destAl = new Alignment((SequenceI[]) newview[0]);
- destCs = (ColumnSelection) newview[1];
+ destHCs = (HiddenColumns) newview[1];
newAlignment = true;
// TODO create alignment from result data with propagated
// references.
destAls.add(destAl);
- destColsel.add(destCs);
+ destColsel.add(destHCs);
resultDest.add(AddDataTo.newAlignment);
throw new Error(
- MessageManager
- .getString("error.implementation_error")
+ MessageManager.getString("error.implementation_error")
+ "TODO: ");
}
}
}
else
{
- Cache.log
- .warn("Couldn't resolve original sequence for new sequence.");
+ Cache.log.warn(
+ "Couldn't resolve original sequence for new sequence.");
}
}
if (sg.hasSeqrep())
{
// adjust boundaries of recovered group w.r.t. new group being
// merged on to original alignment.
- int start = sg.getStartRes() + contigs[ncnt], end = sg
- .getEndRes() + contigs[ncnt];
+ int start = sg.getStartRes() + contigs[ncnt],
+ end = sg.getEndRes() + contigs[ncnt];
if (start < exsg.getStartRes())
{
exsg.setStartRes(start);
grass = groupNames.get(alan[nrj][an].groupRef.getName());
if (grass == null)
{
- Cache.log
- .error("Couldn't relocate group referemce for group "
+ Cache.log.error(
+ "Couldn't relocate group referemce for group "
+ alan[nrj][an].groupRef.getName());
}
}
visan.sequenceRef = sqass;
visAlAn.add(visan);
}
- if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
+ if (contigs[ncnt]
+ + alan[nrj][an].annotations.length > visan.annotations.length)
{
// increase width of annotation row
Annotation[] newannv = new Annotation[contigs[ncnt]
{
// TODO: process each newick file, lifting over sequence refs to
// current alignment, if necessary.
- Cache.log
- .error("Tree recovery from restjob not yet implemented.");
+ Cache.log.error(
+ "Tree recovery from restjob not yet implemented.");
}
}
}
for (AddDataTo action : resultDest)
{
AlignmentI destal;
- ColumnSelection destcs;
- String alTitle = MessageManager.formatMessage(
- "label.webservice_job_title_on", new String[] {
- restClient.service.details.Action,
+ HiddenColumns destcs;
+ String alTitle = MessageManager
+ .formatMessage("label.webservice_job_title_on", new String[]
+ { restClient.service.details.Action,
restClient.service.details.Name, restClient.viewTitle });
switch (action)
{
destcs = destColsel.get(als);
destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- PaintRefresher.Refresh(destaf, destaf.getViewport()
- .getSequenceSetId());
+ PaintRefresher.Refresh(destaf,
+ destaf.getViewport().getSequenceSetId());
// todo transfer any feature settings and colouring
/*
* destaf.getFeatureRenderer().transferSettings(this.featureSettings);
{
if (start + width < end)
{
- blocks[c][s] = sequenceIs[s].getSubSequence(start, start
- + width);
+ blocks[c][s] = sequenceIs[s].getSubSequence(start,
+ start + width);
}
else
{
git://source.jalview.org / jalview.git / commitdiff