label.colourScheme_t-coffeescores = T-Coffee Scores
label.colourScheme_rnahelices = By RNA Helices
label.colourScheme_sequenceid = Sequence ID Colour
- label.colourScheme_gecos\:flower = gecos Flower
- label.colourScheme_gecos\:blossom = gecos Blossom
- label.colourScheme_gecos\:sunset = gecos Sunset
- label.colourScheme_gecos\:ocean = gecos Ocean
+ label.colourScheme_gecos-flower = gecos Flower
+ label.colourScheme_gecos-blossom = gecos Blossom
+ label.colourScheme_gecos-sunset = gecos Sunset
+ label.colourScheme_gecos-ocean = gecos Ocean
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.alignment_output_command = Alignment output - {0}
label.annotations = Annotations
label.structure_options = Structure Options
+label.structure_import_options = Structure Import Options
label.features = Features
label.overview_params = Overview {0}
label.paste_newick_file = Paste Newick file
label.tftype_plddt = pLDDT
label.optional = (optional)
label.choose_tempfac_type = Choose Temperature Factor type
+label.interpret_tempfac_as = Interpret Temperature Factor as
label.add_pae_matrix_file = Add PAE matrix file
label.nothing_selected = Nothing selected
+label.working_ellipsis = Working ...
package jalview.datamodel;
import java.awt.Color;
+import java.math.BigInteger;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
+import java.util.Spliterator;
import java.util.StringTokenizer;
import jalview.bin.Console;
}
@Override
- public boolean hasReferenceSeq()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public SequenceI getReferenceSeq()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
public String getAnnotLabel()
{
return "Contact Matrix";
{
return "Contact Matrix";
}
--
- List<BitSet> groups = null;
-
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- colorMap = new HashMap<>();
- }
-
- @Override
- public boolean hasGroups()
- {
- return groups != null && groups.size() > 0;
- }
-
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- @Override
- public BitSet getGroupsFor(int column)
- {
- for (BitSet gp : groups)
- {
- if (gp.get(column))
- {
- return gp;
- }
- }
- return ContactMatrixI.super.getGroupsFor(column);
- }
-
- HashMap<BitSet, Color> colorMap = new HashMap<>();
-
+ GroupSet grps = new GroupSet();
-
@Override
- public Color getColourForGroup(BitSet bs)
+ public GroupSetI getGroupSet()
{
- if (bs == null)
- {
- return Color.white;
- }
- Color groupCol = colorMap.get(bs);
- if (groupCol == null)
- {
- return Color.white;
- }
- return groupCol;
+ return grps;
}
--
@Override
- public void setColorForGroup(BitSet bs, Color color)
+ public void setGroupSet(GroupSet makeGroups)
{
- colorMap.put(bs, color);
+ grps = makeGroups;
}
--
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
float[][] vals = new float[cols][rows];
StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
int c = 0, r = 0;
--
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
}
if (c >= vals.length)
{
--
break;
}
}
Console.warn(
"Ignoring additional elements for Float string to contact matrix parsing.");
}
--
return vals;
}
}
float getMax();
- boolean hasReferenceSeq();
-
- SequenceI getReferenceSeq();
-
String getAnnotDescr();
String getAnnotLabel();
String getType();
int getWidth();
--
int getHeight();
-
+ public GroupSetI getGroupSet();
+
+ /// proxy methods to simplify use of the interface
+ /// Mappable contact matrices can override these to perform mapping
+
+ default public boolean hasGroupSet()
+ {
+ return getGroupSet() != null;
+ }
default boolean hasGroups()
{
- return false;
+ return hasGroupSet() && getGroupSet().hasGroups();
}
default BitSet getGroupsFor(int column)
{
- BitSet colbitset = new BitSet();
- colbitset.set(column);
- return colbitset;
+ if (!hasGroupSet())
+ {
+ BitSet colbitset = new BitSet();
+ colbitset.set(column);
+ return colbitset;
+ }
+ return getGroupSet().getGroupsFor(column);
}
default List<BitSet> getGroups()
{
- return Arrays.asList();
+ if (!hasGroupSet())
+ {
+ return Arrays.asList();
+ }
+ return getGroupSet().getGroups();
}
default boolean hasTree()
{
- return false;
+ return hasGroupSet() ? getGroupSet().hasTree() : false;
}
/**
*/
default String getNewick()
{
- return null;
+ return hasGroupSet() ? getGroupSet().getNewick() : null;
}
default String getTreeMethod()
{
- return null;
+ return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
}
default boolean hasCutHeight()
{
- return false;
+ return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
}
default double getCutHeight()
{
- return 0;
+ return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
}
- void updateGroups(List<BitSet> colGroups);
+ default void updateGroups(List<BitSet> colGroups)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().updateGroups(colGroups);
+ }
+ }
- void setColorForGroup(BitSet bs, Color color);
+ default void setColorForGroup(BitSet bs, Color color)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().setColorForGroup(bs, color);
+ }
+ }
default Color getColourForGroup(BitSet bs)
{
- return Color.white;
- };
+ if (hasGroupSet())
+ {
+ return getGroupSet().getColourForGroup(bs);
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+
+ void setGroupSet(GroupSet makeGroups);
-
}
import java.util.HashMap;
import java.util.List;
+import jalview.util.MapList;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
-
/**
* Dummy contact matrix based on sequence distance
*
* @author jprocter
*
*/
-public class SeqDistanceContactMatrix implements ContactMatrixI
+public class SeqDistanceContactMatrix
+ extends MappableContactMatrix<SeqDistanceContactMatrix>
+ implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
--
private int width = 0;
public SeqDistanceContactMatrix(int width)
}
@Override
- public boolean hasReferenceSeq()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public SequenceI getReferenceSeq()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
public String getAnnotDescr()
{
return "Sequence distance matrix";
{
return width;
}
--
- private List<BitSet> groups = null;
-
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- }
-
@Override
- public boolean hasGroups()
+ protected double getElementAt(int _column, int i)
{
- return groups != null;
+ return Math.abs(_column - i);
}
--
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- HashMap<BitSet, Color> colorMap = new HashMap<>();
-
@Override
- public Color getColourForGroup(BitSet bs)
+ protected SeqDistanceContactMatrix newMappableContactMatrix(
+ SequenceI newRefSeq, MapList newFromMapList)
{
- if (bs == null)
- {
- return Color.white;
- }
- Color groupCol = colorMap.get(bs);
- if (groupCol == null)
- {
- return Color.white;
- }
- return groupCol;
- }
- @Override
- public void setColorForGroup(BitSet bs, Color color)
- {
- colorMap.put(bs, color);
+ return new SeqDistanceContactMatrix(width);
}
}
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.datamodel.annotations.AnnotationRowBuilder;
import jalview.io.DataSourceType;
- import jalview.io.FileFormatException;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
super(inFile, sourceType, tempfacType);
}
+ public JmolParser(FileParse fp, boolean doXferSettings) throws IOException
+ {
+ super(fp, doXferSettings);
+ }
-
public JmolParser(FileParse fp) throws IOException
{
super(fp);
@Override
public void parse() throws IOException
{
+ parse(true);
+ }
+
+ @Override
+ public void parse(boolean doXferSettings) throws IOException
+ {
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
? PDBEntry.Type.MMCIF.toString()
: "PDB");
- transformJmolModelToJalview(jmolModel.ms);
+ transformJmolModelToJalview(jmolModel.ms, doXferSettings);
}
}
return false;
}
- public void transformJmolModelToJalview(ModelSet ms) throws IOException
+ public void transformJmolModelToJalview(ModelSet ms,
+ boolean localDoXferSettings) throws IOException
{
try
{
}
lastID = tmpatom.resNumIns.trim();
}
- if (isParseImmediately())
+ if (isParseImmediately() && localDoXferSettings)
{
// configure parsing settings from the static singleton
xferSettings();
{
try
{
- Console.info("retrieving pAE for " + pdbId);
+ Console.info("Retrieving PAE for " + pdbId);
File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null);
this.setPAEMatrix(paeFile.getAbsolutePath());
} catch (Throwable t)
// add a PAEMatrix if set (either by above or otherwise)
if (hasPAEMatrix())
{
- Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
- EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
- null, false, false, null);
-
- if (al.getAlignmentAnnotation() != null)
+ try
{
- for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+ Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
+ EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
- null, false, false);
++ null, false, false, null);
+
+ if (al.getAlignmentAnnotation() != null)
{
- annotations.add(alann);
+ for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+ {
+ annotations.add(alann);
+ }
}
+ } catch (Throwable ff)
+ {
+ Console.error("Couldn't import PAE Matrix from " + getPAEMatrix(),
+ ff);
+ warningMessage += "Couldn't import PAE Matrix"
+ + getNewlineString() + ff.getLocalizedMessage()
+ + getNewlineString();
}
}
-
} catch (OutOfMemoryError er)
{
System.out.println(
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- if (evt.isControlDown())
+ // double click selects the whole group
+ if (evt.getClickCount() == 2)
{
ContactMatrixI matrix = av.getContactMatrix(clicked);
{
SequenceI rseq = clicked.sequenceRef;
BitSet grp = matrix.getGroupsFor(currentX);
+ // TODO: cXci needs to be mapped to real groups
for (int c = fr; c <= to; c++)
{
BitSet additionalGrp = matrix.getGroupsFor(c);
{
// select corresponding range in segment under mouse
{
- for (int c = fr; c <= to; c++)
+ int[] rng = forCurrentX.getMappedPositionsFor(fr, to);
+ if (rng != null)
{
- av.getColumnSelection().addElement(c);
+ av.getColumnSelection().addRangeOfElements(rng, true);
}
av.getColumnSelection().addElement(currentX);
}
// PAE SPECIFIC
// and also select everything lower than the max range adjacent
// (kind of works)
- if (PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+ if (evt.isControlDown()
+ && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
{
int c = fr - 1;
ContactRange cr = forCurrentX.getRangeFor(fr, to);
if (// cr.getMin() <= cval &&
cval <= thresh)
{
- av.getColumnSelection().addElement(c--);
- }
- else
- {
- break;
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
+ else
+ {
+ break;
+ }
}
+ c--;
}
c = to;
while (c < forCurrentX.getContactHeight())
if (// cr.getMin() <= cval &&
cval <= thresh)
{
- av.getColumnSelection().addElement(c++);
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
}
else
{
break;
}
+ c++;
+
}
}
}
int fr, to;
fr = Math.min(lastXci.cStart, lastXci.cEnd);
to = Math.max(lastXci.cStart, lastXci.cEnd);
- jalview.bin.Console.trace("Marking " + fr + " to " + to);
- for (int c = fr; c <= to; c++)
+ int[] mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
{
- if (cma.sequenceRef != null)
+ jalview.bin.Console.trace("Marking " + fr + " to " + to
+ + " mapping to sequence positions " + mappedPos[0] + " to "
+ + mappedPos[1]);
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
{
- int col = cma.sequenceRef.findIndex(c);
- av.getColumnSelection().addElement(col);
- }
- else
- {
- av.getColumnSelection().addElement(c);
+ for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
+ // {
+ // if (cma.sequenceRef != null)
+ // {
+ // int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+ // av.getColumnSelection().addElement(col);
+ // }
+ // else
+ {
+ av.getColumnSelection().addElement(c);
+ }
}
}
+ // and again for most recent corner of drag
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- jalview.bin.Console.trace("Marking " + fr + " to " + to);
- for (int c = fr; c <= to; c++)
+ mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
{
- if (cma.sequenceRef != null)
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
{
- int col = cma.sequenceRef.findIndex(c);
- av.getColumnSelection().addElement(col);
- }
- else
- {
- av.getColumnSelection().addElement(c);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to
+ + " mapping to sequence positions " + mappedPos[pair]
+ + " to " + mappedPos[pair + 1]);
+ for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
+ {
+ // if (cma.sequenceRef != null)
+ // {
+ // int col =
+ // cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+ // av.getColumnSelection().addElement(col);
+ // }
+ // else
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ }
}
}
fr = Math.min(lastX, currentX);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
+
int col = ann.sequenceRef.findPosition(column);
+ int[][] highlightPos;
+ int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd);
+ if (mappedPos != null)
+ {
+ highlightPos = new int[1 + mappedPos.length][2];
+ highlightPos[0] = new int[] { col, col };
+ for (int p = 0, h = 0; p < mappedPos.length; h++, p += 2)
+ {
+ highlightPos[h][0] = ann.sequenceRef
+ .findPosition(mappedPos[p] - 1);
+ highlightPos[h][1] = ann.sequenceRef
+ .findPosition(mappedPos[p + 1] - 1);
+ }
+ }
+ else
+ {
+ highlightPos = new int[][] { new int[] { col, col } };
+ }
ap.getStructureSelectionManager()
- .highlightPositionsOn(ann.sequenceRef, new int[][]
- { new int[] { col, col },
- new int[]
- { ci.cStart, ci.cEnd } }, null);
+ .highlightPositionsOn(ann.sequenceRef, highlightPos, null);
}
}
return tooltip;
return;
}
}
- imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
- + 1) * av.getCharWidth();
+ updateFadedImageWidth();
if (imgWidth < 1)
{
return;
g.drawImage(image, 0, 0, this);
}
+ public void updateFadedImageWidth()
+ {
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+ + 1) * av.getCharWidth();
+
+ }
+
/**
* set true to enable redraw timing debug output on stderr
*/
@Override
public int getFadedImageWidth()
{
+ updateFadedImageWidth();
return imgWidth;
}
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
+ import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Locale;
+ import java.util.Map;
import java.util.concurrent.Callable;
import java.util.concurrent.Executors;
import com.stevesoft.pat.Regex;
+ import jalview.analysis.AlignmentUtils;
+ import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
+ import jalview.datamodel.AlignmentAnnotation;
+ import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
+ import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
import jalview.fts.api.FTSData;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.fts.service.threedbeacons.TDB_FTSData;
+ import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
import jalview.gui.structurechooser.StructureChooserQuerySource;
import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.FilterOption;
import jalview.util.StringUtils;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.sifts.SiftsSettings;
}
/**
- * Handles action event for btn_pdbFromFile
+ * Handles action event for btn_paeMatrixFile
*/
@Override
protected void paeMatrixFile_actionPerformed()
"label.load_pae_matrix_file_associate_with_structure",
pdbFile.getName()));
+ // TODO convert to Callable/Promise
int value = chooser.showOpenDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
+ String fileName = chooser.getSelectedFile().getPath();
+ try
+ {
+ PAEContactMatrix.validateContactMatrixFile(fileName);
+ } catch (Exception thr)
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_load_file", new Object[]
+ { fileName }) + "<br>" + thr.getLocalizedMessage(),
+ MessageManager.getString("label.error_loading_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ Console.error("Couldn't import " + fileName + " as a PAE matrix",
+ thr);
+ return;
+ }
+ localPdbPaeMatrixFileName = fileName;
Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
}
validateAssociationFromFile();
{
pdbFileString = MessageManager.getString("label.none");
pdbFileTooltip = MessageManager.getString("label.nothing_selected");
+ setPdbOptionsEnabled(false);
}
}
else
{
btn_pdbFromFile.setEnabled(false);
+ setPdbOptionsEnabled(false);
// lbl_fromFileStatus.setIcon(errorImage);
pdbFileString = MessageManager.getString("label.none");
pdbFileTooltip = MessageManager.getString("label.nothing_selected");
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final int preferredHeight = pnl_filter.getHeight();
+ btn_add.setEnabled(false);
+ btn_newView.setEnabled(false);
+ btn_cancel.setEnabled(false);
+ actionsPanel.setEnabled(false);
+ final String progress = MessageManager
+ .getString("label.working_ellipsis");
+ setProgressBar(progress, progress.hashCode());
Runnable viewStruc = new Runnable()
{
@Override
.getCmb_assSeq().getSelectedItem();
SequenceI userSelectedSeq = assSeqOpt.getSequence();
if (userSelectedSeq != null)
+ {
selectedSequence = userSelectedSeq;
+ }
String pdbFilename = selectedPdbFileName;
StructureChooser.openStructureFileForSequence(ssm, sc, ap,
- selectedSequence, true, pdbFilename, tft, paeFilename);
+ selectedSequence, true, pdbFilename, tft, paeFilename,
+ true);
}
SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
+ setProgressBar("Complete.", progress.hashCode());
closeAction(preferredHeight);
mainFrame.dispose();
}
StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
+ return launchStructureViewer(ssm, pdbEntriesToView, alignPanel,
+ sequences, null);
+ }
+
+ private StructureViewer launchStructureViewer(
+ StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences,
+ ViewerType viewerType)
+ {
long progressId = sequences.hashCode();
setProgressBar(MessageManager
.getString("status.launching_3d_structure_viewer"), progressId);
MessageManager.getString(
"status.fetching_3d_structures_for_selected_entries"),
progressId);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel,
+ viewerType);
}
else
{
"status.fetching_3d_structures_for",
pdbEntriesToView[0].getId()), progressId);
// Can we pass a pre-computeMappinged pdbFile?
- theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel,
+ viewerType);
}
setProgressBar(null, progressId);
// remember the last viewer we used...
public static void openStructureFileForSequence(
StructureSelectionManager ssm, StructureChooser sc,
AlignmentPanel ap, SequenceI seq, boolean prompt,
- String sFilename, TFType tft, String paeFilename)
+ String sFilename, TFType tft, String paeFilename,
+ boolean doXferSettings)
{
- boolean headless = false;
+ openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft,
+ paeFilename, false, true, doXferSettings, null);
+ }
+
+ public static void openStructureFileForSequence(
+ StructureSelectionManager ssm, StructureChooser sc,
+ AlignmentPanel ap, SequenceI seq, boolean prompt,
+ String sFilename, TFType tft, String paeFilename,
+ boolean forceHeadless, boolean showRefAnnotations,
+ boolean doXferSettings, ViewerType viewerType)
+ {
+ boolean headless = forceHeadless;
if (sc == null)
{
- headless = true;
+ // headless = true;
+ prompt = false;
sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
}
if (ssm == null)
PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
- tft, paeFilename);
+ tft, paeFilename, doXferSettings);
- StructureViewer sViewer = sc.launchStructureViewer(ssm,
- new PDBEntry[]
- { fileEntry }, ap, new SequenceI[] { seq });
+ // if headless, "false" in the sc constructor above will avoid GUI behaviour
+ // in sc.launchStructureViewer()
+ if (!headless && !(viewerType == null))
+ sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[]
+ { seq }, viewerType);
if (headless)
sc.mainFrame.dispose();
+
+ if (showRefAnnotations)
+ showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+ }
+
+ public static void showReferenceAnnotationsForSequence(AlignFrame af,
+ SequenceI sequence)
+ {
+ AlignViewport av = af.getCurrentView();
+ AlignmentI al = av.getAlignment();
+
+ List<SequenceI> forSequences = new ArrayList<>();
+ forSequences.add(sequence);
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, null,
+ candidates, al);
+ final SequenceGroup selectionGroup = av.getSelectionGroup();
+ AlignmentUtils.addReferenceAnnotations(candidates, al, selectionGroup);
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ // required to readjust the height and position of the PAE
+ // annotation
+ ap.adjustAnnotationHeight();
+ }
+
}
}
import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactMatrixI;
import jalview.structure.SelectionSource;
import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.ws.datamodel.MappableContactMatrixI;
/**
* DOCUMENT ME!
cm.setColorForGroup(gp, colors.get(gp));
}
}
+ // stash colors in linked annotation row.
+ // doesn't work yet. TESTS!
+ int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+ : 0;
+ Annotation ae;
+ Color gpcol = null;
+ int[] seqpos = null;
+ for (BitSet gp : colors.keySet())
+ {
+ gpcol = colors.get(gp);
+ for (int p = gp.nextSetBit(0); p >= 0
+ && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+ {
+ if (cm instanceof MappableContactMatrixI)
+ {
+ MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
+ seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+ if (seqpos == null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ ae = aa.getAnnotationForPosition(seqpos[0]);
+ }
+ else
+ {
+ ae = aa.getAnnotationForPosition(p + sstart);
+ }
+ if (ae != null)
+ {
+ ae.colour = gpcol.brighter().darker();
+ }
+ }
+ }
}
}
return false;
}
ColumnSelection cs = av.getColumnSelection();
--
HiddenColumns hc = av.getAlignment().getHiddenColumns();
int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
: colm;
}
return false;
}
--
private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
{
BitSet gp = new BitSet();
Color col)
{
SequenceI rseq = tp.assocAnnotation.sequenceRef;
-
if (av == null || av.getAlignment() == null)
{
// alignment is closed
{
continue;
}
+ // TODO - sort indices for faster lookup
-
ColumnSelection cs = av.getColumnSelection();
HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
+ MappableContactMatrixI mcm = null;
+ int offp;
+ if (cm instanceof MappableContactMatrixI)
+ {
+ mcm = (MappableContactMatrixI) cm;
+ int[] seqpos = mcm.getMappedPositionsFor(
+ tp.assocAnnotation.sequenceRef, colm);
+ if (seqpos == null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ offp = seqpos[0];
+ }
+ else
{
- int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+ offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
: colm;
-
- if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+ }
+ if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+ {
+ if (cs.contains(offp - 1))
{
- if (cs.contains(offp - 1))
- {
- cs.removeElement(offp - 1);
- }
- else
- {
- cs.addElement(offp - 1);
- }
+ cs.removeElement(offp - 1);
+ }
+ else
+ {
+ cs.addElement(offp - 1);
}
}
}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.ws.datamodel.MappableContactMatrixI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.MapListType;
import jalview.xml.binding.jalview.MapListType.MapListFrom;
import jalview.xml.binding.jalview.MapListType.MapListTo;
import jalview.xml.binding.jalview.Mapping;
{
for (BitSet gp : cm.getGroups())
{
- BigInteger val = new BigInteger(gp.toByteArray());
- xmlmat.getGroups().add(val.toString());
+ xmlmat.getGroups().add(stringifyBitset(gp));
}
}
if (cm.hasTree())
{
xmlmat.setCutHeight(cm.getCutHeight());
}
--
// set/get properties
+ if (cm instanceof MappableContactMatrixI)
+ {
+ jalview.util.MapList mlst = ((MappableContactMatrixI) cm)
+ .getMapFor(annotation.sequenceRef);
+ if (mlst != null)
+ {
+ MapListType mp = new MapListType();
+ List<int[]> r = mlst.getFromRanges();
+ for (int[] range : r)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(range[0]);
+ mfrom.setEnd(range[1]);
+ // mp.addMapListFrom(mfrom);
+ mp.getMapListFrom().add(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int[] range : r)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(range[0]);
+ mto.setEnd(range[1]);
+ // mp.addMapListTo(mto);
+ mp.getMapListTo().add(mto);
+ }
+ mp.setMapFromUnit(
+ BigInteger.valueOf(mlst.getFromRatio()));
+ mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+ xmlmat.setMapping(mp);
+ }
+ }
+ // and add to model
an.getContactmatrix().add(xmlmat);
}
}
}
+ private String stringifyBitset(BitSet gp)
+ {
+ StringBuilder sb = new StringBuilder();
+ for (long val : gp.toLongArray())
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(val);
+ }
+ return sb.toString();
+ }
+
+ private BitSet deStringifyBitset(String stringified)
+ {
+ if ("".equals(stringified) || stringified == null)
+ {
+ return new BitSet();
+ }
+ String[] longvals = stringified.split(",");
+ long[] newlongvals = new long[longvals.length];
+ for (int lv = 0; lv < longvals.length; lv++)
+ {
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
+ } catch (Exception x)
+ {
+ errorMessage += "Couldn't destringify bitset from: '" + stringified
+ + "'";
+ newlongvals[lv] = 0;
+ }
+ }
+ return BitSet.valueOf(newlongvals);
+
+ }
-
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
.fromFloatStringToContacts(xmlmat.getElements(),
xmlmat.getCols().intValue(),
xmlmat.getRows().intValue());
+ jalview.util.MapList mapping = null;
+ if (xmlmat.getMapping() != null)
+ {
+ MapListType m = xmlmat.getMapping();
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFrom().size() * 2];
+ Iterator<MapListFrom> from = m.getMapListFrom()
+ .iterator();// enumerateMapListFrom();
+ for (int _i = 0; from.hasNext(); _i += 2)
+ {
+ MapListFrom mf = from.next();
+ fr[_i] = mf.getStart();
+ fr[_i + 1] = mf.getEnd();
+ }
+ int fto[] = new int[m.getMapListTo().size() * 2];
+ Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
+ for (int _i = 0; to.hasNext(); _i += 2)
+ {
+ MapListTo mf = to.next();
+ fto[_i] = mf.getStart();
+ fto[_i + 1] = mf.getEnd();
+ }
- PAEContactMatrix newpae = new PAEContactMatrix(
- jaa.sequenceRef, elements);
+ mapping = new jalview.util.MapList(fr, fto,
+ m.getMapFromUnit().intValue(),
+ m.getMapToUnit().intValue());
+ }
List<BitSet> newgroups = new ArrayList<BitSet>();
if (xmlmat.getGroups().size() > 0)
{
for (String sgroup : xmlmat.getGroups())
{
- try
- {
- BigInteger group = new BigInteger(sgroup);
- newgroups.add(BitSet.valueOf(group.toByteArray()));
- } catch (NumberFormatException nfe)
- {
- Console.error(
- "Problem parsing groups for a contact matrix (\""
- + sgroup + "\"",
- nfe);
- }
+ newgroups.add(deStringifyBitset(sgroup));
}
}
String nwk = xmlmat.getNewick().size() > 0
Console.log.info(
"Ignoring additional clusterings for contact matrix");
}
--
String treeMethod = xmlmat.getTreeMethod();
double thresh = xmlmat.getCutHeight() != null
? xmlmat.getCutHeight()
: 0;
- newpae.restoreGroups(newgroups, treeMethod, nwk, thresh);
+ GroupSet grpset = new GroupSet();
+ grpset.restoreGroups(newgroups, treeMethod, nwk, thresh);
+ PAEContactMatrix newpae = new PAEContactMatrix(
+ jaa.sequenceRef, mapping, elements, grpset);
jaa.sequenceRef.addContactListFor(jaa, newpae);
}
}
* shown when no data available from map
*/
Color no_data;
--
/**
* shown for region not currently visible - should normally not see this
*/
Color hidden;
--
/**
* linear shading scheme min/max
*/
x++;
continue;
}
+ // ContactListI from viewport can map column -> group
Color gpcol = (cm == null) ? Color.white
- : cm.getColourForGroup(cm.getGroupsFor(column));
+ : contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
// feature still in development - highlight or omit regions hidden in
// the alignment - currently marks them as red rows
boolean maskHiddenCols = false;
- // TODO: pass visible column mask to the ContactGeometry object so it maps
+ // TODO: optionally pass visible column mask to the ContactGeometry object
+ // so it maps
// only visible contacts to geometry
// Bean holding mapping from contact list to pixels
+ // TODO: allow bracketing/limiting of range on contacts to render (like
+ // visible column mask but more flexible?)
+
+ // COntactListI provides mapping for column -> cm-groupmapping
final ContactGeometry cgeom = new ContactGeometry(contacts,
_aa.graphHeight);
for (int ht = y2, eht = y2
- _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
{
-
ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
y2 - ht + cgeom.pixels_step);
// cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
boolean rowsel = false, containsHidden = false;
if (columnSelection != null)
{
- if (_aa.sequenceRef == null)
- {
- rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
- }
- else
- {
- // TODO check we have correctly mapped cstart to local sequence
- // numbering
- int s = _aa.sequenceRef.findIndex(ci.cStart);
- int e = _aa.sequenceRef.findIndex(ci.cEnd);
- if (maskHiddenCols && hasHiddenColumns)
- {
- // TODO: turn into function and create test !!
- Iterator<int[]> viscont = hiddenColumns
- .getVisContigsIterator(s, e, false);
- containsHidden = !viscont.hasNext();
- }
- if (s > 0 && s < _aa.sequenceRef.getLength())
- {
- rowsel = columnSelection.intersects(s, e);
- }
-
- }
+ rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+ maskHiddenCols);
}
// TODO: show selected region
if (colsel || rowsel)
(int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
}
g.setColor(col);
--
if (cgeom.pixels_step > 1)
{
g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
package jalview.ws.datamodel.alphafold;
import java.awt.Color;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
+
+import org.json.simple.JSONObject;
import jalview.analysis.AverageDistanceEngine;
import jalview.bin.Console;
+import jalview.datamodel.Annotation;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileParse;
+import jalview.util.MapList;
import jalview.util.MapUtils;
+import jalview.ws.dbsources.EBIAlfaFold;
-public class PAEContactMatrix implements ContactMatrixI
+public class PAEContactMatrix extends
+ MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
{
+
- SequenceI refSeq = null;
-
- /**
- * the length that refSeq is expected to be (excluding gaps, of course)
- */
- int length;
+
int maxrow = 0, maxcol = 0;
- int[] indices1, indices2;
+
float[][] elements;
float maxscore;
- private void setRefSeq(SequenceI _refSeq)
- {
- refSeq = _refSeq;
- while (refSeq.getDatasetSequence() != null)
- {
- refSeq = refSeq.getDatasetSequence();
- }
- length = _refSeq.getEnd() - _refSeq.getStart() + 1;
- }
+
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+ throws FileFormatException
{
setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
}
/**
+ * new matrix with specific mapping to a reference sequence
+ *
+ * @param newRefSeq
+ * @param newFromMapList
+ * @param elements2
+ * @param grps2
+ */
+ public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
+ float[][] elements2, GroupSet grps2)
+ {
+ this(newRefSeq, elements2);
+ toSeq = newFromMapList;
+ grps = grps2;
+ }
+
+ /**
* parse a sane JSON representation of the pAE
*
* @param pae_obj
@SuppressWarnings("unchecked")
private void parse_version_2_pAE(Map<String, Object> pae_obj)
{
- // this is never going to be reached by the integer rounding.. or is it ?
- maxscore = ((Double) MapUtils.getFirst(pae_obj,
- "max_predicted_aligned_error", "max_pae")).floatValue();
+ maxscore = -1;
+ // look for a maxscore element - if there is one...
+ try
+ {
+ // this is never going to be reached by the integer rounding.. or is it ?
+ maxscore = ((Double) MapUtils.getFirst(pae_obj,
+ "max_predicted_aligned_error", "max_pae")).floatValue();
+ } catch (Throwable t)
+ {
+ // ignore if a key is not found.
+ }
List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
.getFirst(pae_obj, "predicted_aligned_error", "pae"));
elements = new float[scoreRows.size()][scoreRows.size()];
while (scores.hasNext())
{
Object d = scores.next();
-
if (d instanceof Double)
+ {
elements[row][col++] = ((Double) d).longValue();
+ }
else
+ {
elements[row][col++] = (float) ((Long) d).longValue();
+ }
+
+ if (maxscore < elements[row][col - 1])
+ {
+ maxscore = elements[row][col - 1];
+ }
}
row++;
col = 0;
// dataset refSeq
Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
+ // two pass - to allocate the elements array
+ while (rows.hasNext())
+ {
+ int row = rows.next().intValue();
+ int col = cols.next().intValue();
+ if (maxrow < row)
+ {
+ maxrow = row;
+ }
+ if (maxcol < col)
+ {
+ maxcol = col;
+ }
+
+ }
+ rows = ((List<Long>) pae_obj.get("residue1")).iterator();
+ cols = ((List<Long>) pae_obj.get("residue2")).iterator();
Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
.iterator();
- // assume square matrix
- elements = new float[length][length];
+ elements = new float[maxrow][maxcol];
while (scores.hasNext())
{
float escore = scores.next().floatValue();
}
@Override
- public ContactListI getContactList(final int _column)
+ public ContactListI getContactList(final int column)
{
- // final int _column;
- // if (toSeq != null)
- // {
- // int[] word = toSeq.locateInTo(column, column);
- // if (word == null)
- // {
- // return null;
- // }
- // _column = word[0];
- // }
- // else
- // {
- // _column = column;
- // }
- if (_column < 0 || _column >= elements.length)
+ if (column < 0 || column >= elements.length)
{
return null;
}
@Override
public int getPosition()
{
- return _column;
+ return column;
}
@Override
}
@Override
- public double getContactAt(int column)
+ public double getContactAt(int mcolumn)
{
- if (column < 0 || column >= elements[_column].length)
+ if (mcolumn < 0 || mcolumn >= elements[column].length)
{
return -1;
}
- return elements[_column][column];
+ return elements[column][mcolumn];
}
});
}
@Override
- public float getMin()
+ protected double getElementAt(int _column, int i)
{
- return 0;
+ return elements[_column][i];
}
@Override
- public float getMax()
- {
- return maxscore;
- }
-
- @Override
- public boolean hasReferenceSeq()
+ public float getMin()
{
- return (refSeq != null);
+ return 0;
}
@Override
- public SequenceI getReferenceSeq()
+ public float getMax()
{
- return refSeq;
+ return maxscore;
}
@Override
{
return length;
}
--
- List<BitSet> groups = null;
-
- @Override
- public boolean hasGroups()
- {
- return groups != null;
- }
-
- String newick = null;
-
- @Override
- public String getNewick()
- {
- return newick;
- }
-
- @Override
- public boolean hasTree()
- {
- return newick != null && newick.length() > 0;
- }
-
- boolean abs;
-
- double thresh;
-
- String treeType = null;
-
- public void makeGroups(float thresh, boolean abs)
+ public static void validateContactMatrixFile(String fileName)
+ throws FileFormatException, IOException
{
- AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
- this);
- double height = clusterer.findHeight(clusterer.getTopNode());
- newick = new jalview.io.NewickFile(clusterer.getTopNode(), false, true)
- .print();
- treeType = "UPGMA";
- Console.trace("Newick string\n" + newick);
-
- List<BinaryNode> nodegroups;
- if (abs ? height > thresh : 0 < thresh && thresh < 1)
+ FileInputStream infile = null;
+ try
{
- float cut = abs ? (float) (thresh / height) : thresh;
- Console.debug("Threshold " + cut + " for height=" + height);
-
- nodegroups = clusterer.groupNodes(cut);
- }
- else
+ infile = new FileInputStream(new File(fileName));
+ } catch (Throwable t)
{
- nodegroups = new ArrayList<BinaryNode>();
- nodegroups.add(clusterer.getTopNode());
+ new IOException("Couldn't open " + fileName, t);
}
-
- this.abs = abs;
- this.thresh = thresh;
- groups = new ArrayList<>();
- for (BinaryNode root : nodegroups)
+ JSONObject paeDict = null;
+ try
{
- BitSet gpset = new BitSet();
- for (BinaryNode leaf : clusterer.findLeaves(root))
- {
- gpset.set((Integer) leaf.element());
- }
- groups.add(gpset);
- }
- }
-
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- if (colGroups != null)
+ paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile);
+ } catch (Throwable t)
{
- groups = colGroups;
+ new FileFormatException("Couldn't parse " + fileName
+ + " as a JSON dict or array containing a dict");
}
- }
- @Override
- public BitSet getGroupsFor(int column)
- {
- for (BitSet gp : groups)
+ PAEContactMatrix matrix = new PAEContactMatrix(
+ new SequenceDummy("Predicted"), (Map<String, Object>) paeDict);
+ if (matrix.getWidth() <= 0)
{
- if (gp.get(column))
- {
- return gp;
- }
- }
- return ContactMatrixI.super.getGroupsFor(column);
- }
-
- HashMap<BitSet, Color> colorMap = new HashMap<>();
-
- @Override
- public Color getColourForGroup(BitSet bs)
- {
- if (bs == null)
- {
- return Color.white;
- }
- Color groupCol = colorMap.get(bs);
- if (groupCol == null)
- {
- return Color.white;
+ throw new FileFormatException(
+ "No data in PAE matrix read from '" + fileName + "'");
}
- return groupCol;
- }
-
- @Override
- public void setColorForGroup(BitSet bs, Color color)
- {
- colorMap.put(bs, color);
}
--
- public void restoreGroups(List<BitSet> newgroups, String treeMethod,
- String tree, double thresh2)
- {
- treeType = treeMethod;
- groups = newgroups;
- thresh = thresh2;
- newick = tree;
-
- }
-
- @Override
- public boolean hasCutHeight()
- {
- return groups != null && thresh != 0;
- }
-
- @Override
- public double getCutHeight()
- {
- return thresh;
- }
-
@Override
- public String getTreeMethod()
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
{
- return treeType;
+ PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
+ elements, new GroupSet(grps));
+ return pae;
}
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
File pae = fetchAlphaFoldPAE(id, retrievalUrl);
- addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
}
public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
- int index, String id, boolean isStruct, boolean isStructId)
+ int index, String id, boolean isStruct, boolean isStructId,
+ String label)
{
FileInputStream paeInput = null;
try
if (isStruct)
{
+ // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with
+ // different params.
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
if (ssm != null)
{
String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
- addPAEToStructure(ssm, structFilename, pae);
+ addPAEToStructure(ssm, structFilename, pae, label);
}
}
try
{
if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
- index, id))
+ index, id, label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to sequence.");
}
public static void addPAEToStructure(StructureSelectionManager ssm,
- String structFilename, File pae)
+ String structFilename, File pae, String label)
{
FileInputStream paeInput = null;
try
try
{
- if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput,
+ label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to structure.");
*/
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
- String seqId) throws IOException, ParseException
+ String seqId, String label) throws IOException, ParseException
{
SequenceI sequence = null;
if (seqId == null)
return false;
}
return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
- sequence);
+ sequence, label);
}
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input,
- SequenceI sequence) throws IOException, ParseException
+ SequenceI sequence, String label)
+ throws IOException, ParseException
{
JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
if (paeDict == null)
}
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) paeDict);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
+ matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ if (label != null)
+ cmannot.label = label;
pdbAlignment.addAnnotation(cmannot);
return true;
return paeDict;
}
+ // ###### TEST THIS
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping[] smArray, InputStream paeInput)
+ StructureMapping[] smArray, InputStream paeInput, String label)
throws IOException, ParseException
{
boolean someDone = false;
for (StructureMapping sm : smArray)
{
boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
- paeInput);
+ paeInput, label);
someDone |= thisDone;
}
return someDone;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping sm, InputStream paeInput)
+ StructureMapping sm, InputStream paeInput, String label)
throws IOException, ParseException
{
JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+ SequenceI seq = sm.getSequence();
+ ContactMatrixI matrix = new PAEContactMatrix(seq,
(Map<String, Object>) pae_obj);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
- AlignmentAnnotation cmannot = seq.addContactList(matrix);
+ matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
- sm.getSequence().addAlignmentAnnotation(cmannot);
-
+ /* this already happens in Sequence.addContactList()
+ seq.addAlignmentAnnotation(cmannot);
+ */
return true;
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.03.17 at 05:31:44 PM GMT
+// Generated on: 2023.05.13 at 06:58:41 PM BST
//
++
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
++
/**
* <p>
* Java class for MatrixType complex type.
* <element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/>
* </sequence>
* <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
@XmlType(
name = "MatrixType",
propOrder =
- { "elements", "groups", "newick", "property" })
+ { "elements", "groups", "newick", "property", "mapping" })
public class MatrixType
{
protected List<Property> property;
+ protected MapListType mapping;
+
@XmlAttribute(name = "type", required = true)
protected String type;
}
/**
+ * Gets the value of the mapping property.
+ *
+ * @return possible object is {@link MapListType }
+ *
+ */
+ public MapListType getMapping()
+ {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is {@link MapListType }
+ *
+ */
+ public void setMapping(MapListType value)
+ {
+ this.mapping = value;
+ }
+
+ /**
* Gets the value of the type property.
*
* @return possible object is {@link String }
Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
}
- @Test
+ @Test(groups = { "Functional" })
public void testUPGMAEngine() throws Exception
{
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
}
System.out.println("\\");
}
--
}
}
import java.awt.Rectangle;
import java.io.File;
import java.io.IOException;
+import java.math.BigInteger;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.ws.datamodel.MappableContactMatrixI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
@Test(singleThreaded = true)
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
- dummyMat.makeGroups(0.5f, false);
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
+ // verify store/restore of group bitsets
+ for (BitSet gp : dummyMat.getGroups())
+ {
+ StringBuilder sb = new StringBuilder();
+ for (long val : gp.toLongArray())
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(val);
+ }
+ String[] longvals = sb.toString().split(",");
+ long[] newlongvals = new long[longvals.length];
+ for (int lv = 0; lv < longvals.length; lv++)
+ {
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
+ } catch (Exception x)
+ {
+ Assert.fail("failed to deserialise bitset element ");
+ }
+ }
+ BitSet newGp = BitSet.valueOf(newlongvals);
+ assertTrue(gp.equals(newGp));
+ }
-
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
".jvp");
new Jalview2XML(false).saveState(tfile);
ContactMatrixI restoredMat = newSeq
.getContactMatrixFor(newSeq.getAnnotation()[0]);
Assert.assertNotNull(restoredMat);
+ MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq);
+ MapList newMap = ((MappableContactMatrixI) restoredMat)
+ .getMapFor(newSeq);
+ Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges());
+ Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges());
+ Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio());
+ Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio());
-
for (i = sq.getLength() - 1; i >= 0; i--)
{
ContactListI oldCM = dummyMat.getContactList(i),
newCM = restoredMat.getContactList(i);
for (int j = oldCM.getContactHeight(); j >= 0; j--)
{
- Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
+ double old_j = oldCM.getContactAt(j);
+ double new_j = newCM.getContactAt(j);
+ Assert.assertEquals(old_j, new_j);
}
}
Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
--
}
}
git://source.jalview.org / jalview.git / commitdiff