* @return true if parsing resulted in something being imported to the view or
* dataset
*/
- public boolean parseFeaturesFile(String file, String protocol,
+ public boolean parseFeaturesFile(String file, DataSourceType sourceType,
boolean relaxedIdMatching);
+ /**
+ * mark columns containing highlighted regions (e.g. from search, structure
+ * highlight, or a mouse over event in another viewer)
+ *
+ * @param invert
+ * @param extendCurrent
+ * @param toggle
+ * @return
+ */
+ boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
+ boolean toggle);
+
}
*
* @param file
* file URL, content, or other resolvable path
- * @param paste
- * @param type
++ * @param sourceType
* is protocol for accessing data referred to by file
* @param autoenabledisplay
* when true, display features flag will be automatically enabled if
* features are loaded
* @return true if data parsed as a features file
*/
- public boolean parseFeaturesFile(String file, DataSourceType paste,
- public boolean parseFeaturesFile(String file, String type,
++ public boolean parseFeaturesFile(String file, DataSourceType sourceType,
boolean autoenabledisplay)
{
boolean featuresFile = false;
.getFeatureRenderer().getFeatureColours();
boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
"relaxedidmatch", false);
- featuresFile = new FeaturesFile(file, paste).parse(
- featuresFile = new FeaturesFile(file, type).parse(
++ featuresFile = new FeaturesFile(file, sourceType).parse(
viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
System.err
.println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
- if (protocol == null || protocol.trim().length() == 0
- || protocol.equals("null"))
+ if (protocol == null)
{
- String sourceType = pdb.getProperty().get("protocol");
- protocol = (String) pdb.getProperty("protocol");
++ String sourceType = (String) pdb.getProperty("protocol");
+ try
+ {
+ protocol = DataSourceType.valueOf(sourceType);
+ } catch (IllegalArgumentException e)
+ {
+ // ignore
+ }
if (protocol == null)
{
System.err.println("Couldn't work out protocol to open structure: "
closeViewer();
}
});
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable<String, String>());
- pdbentry.getProperty().put("protocol", protocol.toString());
- }
+ pdbentry.setProperty("protocol", protocol);
-
if (pdbentry.getFile() != null)
++
{
// import structure data from pdbentry.getFile based on given protocol
- if (protocol.equals(AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
// TODO: JAL-623 : correctly record file contents for matching up later
// pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
public AppletJmolBinding(AppletJmol appletJmol,
StructureSelectionManager sSm, PDBEntry[] pdbentry,
- SequenceI[][] seq, String[][] chains, DataSourceType protocol)
- SequenceI[][] seq, String protocol)
++ SequenceI[][] seq, DataSourceType protocol)
{
- super(sSm, pdbentry, seq, chains, protocol);
+ super(sSm, pdbentry, seq, protocol);
appletJmolBinding = appletJmol;
}
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
+ protected ExtJmol(AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
+ PDBEntry[] pdbentry, SequenceI[][] seq,
- String protocol)
+ DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
- chains, protocol);
+ protocol);
}
public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
System.out.println("Creating HTML image: " + file);
continue;
}
- else if (format.equalsIgnoreCase("biojsmsa"))
++ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput
+ .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
+ System.out.println("Creating BioJS MSA Viwer HTML file: "
+ + file);
+ continue;
+ }
- else if (format.equalsIgnoreCase("imgMap"))
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
{
af.createImageMap(new File(file), imageName);
System.out.println("Creating image map: " + file);
private String id;
- private String chainCode;
-
public enum Type
{
- PDB, MMCIF, FILE;
+ // TODO is FILE needed; if not is this needed or can we
+ // use FileFormatI for PDB, MMCIF?
+ PDB("pdb", "xml"), MMCIF("mmcif", "mmcif"), FILE("?", "?");
+ String ext;
+
+ String format;
+
+ private Type(String fmt, String ex)
+ {
+ format = fmt;
+ ext = ex;
+ }
+
+ public String getFormat()
+ {
+ return format;
+ }
+ public String getExtension()
+ {
+ return ext;
+ }
- }
+
- Hashtable<String, String> properties;
+ /**
+ * case insensitive matching for Type enum
+ *
+ * @param value
+ * @return
+ */
+ public static Type getType(String value)
+ {
+ for (Type t : Type.values())
+ {
+ if (t.toString().equalsIgnoreCase(value))
+ {
+ return t;
+ }
+ }
+ return null;
+ }
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
+ /**
+ * case insensitive equivalence for strings resolving to PDBEntry type
+ *
+ * @param t
+ * @return
+ */
+ public boolean matches(String t)
+ {
+ return (this.toString().equalsIgnoreCase(t));
+ }
+ }
+
-
+ /**
+ * Answers true if obj is a PDBEntry with the same id and chain code (both
+ * ignoring case), file, type and properties
*/
@Override
public boolean equals(Object obj)
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.util.StringUtils;
throws IOException
{
URL url = getUrl(ids);
-
+
BufferedReader reader = getHttpResponse(url, ids);
+ if (reader == null)
+ {
+ // request failed
+ return null;
+ }
- FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
+ FileParse fp = new FileParse(reader, url.toString(), DataSourceType.URL);
return fp;
}
public Viewer viewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String protocol)
+ DataSourceType protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+ import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String inFile, DataSourceType sourceType)
- public JmolParser(String inFile, String type) throws IOException
++ public JmolParser(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, FileParse fp) throws IOException
+ public JmolParser(FileParse fp) throws IOException
{
super(fp);
}
private static final String ALPHACARBON = "CA";
+ private List<String> chainNames = new ArrayList<String>();
+
+ private Hashtable<String, String> chainFile = new Hashtable<String, String>();
++
/*
* Object through which we talk to Chimera
*/
* @param ssm
* @param pdbentry
* @param sequenceIs
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- DataSourceType protocol)
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
++ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
viewer = new ChimeraManager(
new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
}
@Override
public void drop(DropTargetDropEvent evt)
{
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
+ List<String> files = new ArrayList<String>();
+ List<DataSourceType> protocols = new ArrayList<DataSourceType>();
try
{
}
if (type != null)
{
- if (FileFormat.PDB.equals(type))
- if (StructureFile.isStructureFile(type))
++ if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type))
{
filesmatched.add(new Object[] { file, protocol, mtch });
continue;
private FeatureRenderer fr = null;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- DataSourceType protocol)
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
++ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
}
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+ import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
public void drop(DropTargetDropEvent evt)
{
boolean success = true;
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- java.util.List<String> files = new ArrayList<String>();
- java.util.List<String> protocols = new ArrayList<String>();
+ List<String> files = new ArrayList<String>();
+ List<DataSourceType> protocols = new ArrayList<DataSourceType>();
try
{
if (v_client != null)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "vdj",
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- new String[] { "Vamsas Document" }, "Vamsas Document");
++ Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ "Vamsas Document", "Vamsas Document");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
*/
public void setVamsasUpdate(boolean b)
{
-- jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
++ Cache.log.debug("Setting gui for Vamsas update "
+ (b ? "in progress" : "finished"));
if (vamUpdate != null)
for (Object file : (List) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
- files.add(((File)file).toString());
+ files.add(((File) file).toString());
- protocols.add(FormatAdapter.FILE);
+ protocols.add(DataSourceType.FILE);
}
}
else
import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
+import jalview.io.FileFormat;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
- import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
private FeatureRenderer fr = null;
+
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains,
- DataSourceType protocol)
- SequenceI[][] sequenceIs, String protocol)
++ SequenceI[][] sequenceIs, DataSourceType protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
cvf = chimeraViewFrame;
}
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
+ import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.DBRefFetcher;
public class StructureChooser extends GStructureChooser implements
IProgressIndicator
{
- private boolean structuresDiscovered = false;
++ private static int MAX_QLENGTH = 7820;
+
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
private boolean isValidPBDEntry;
+ private boolean cachedPDBExists;
+
- private static int MAX_QLENGHT = 7820;
-
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<String>();
- if (seq.getAllPDBEntries() != null)
+ if (seq.getAllPDBEntries() != null
- && queryBuilder.length() < MAX_QLENGHT)
++ && queryBuilder.length() < MAX_QLENGTH)
{
for (PDBEntry entry : seq.getAllPDBEntries())
{
{
for (DBRefEntry dbRef : seq.getDBRefs())
{
- if (isValidSeqName(getDBRefId(dbRef)))
+ if (isValidSeqName(getDBRefId(dbRef))
- && queryBuilder.length() < MAX_QLENGHT)
++ && queryBuilder.length() < MAX_QLENGTH)
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
- .getModelIndex();
+ .getModelIndex();
int[] selectedRows = getResultTable().getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
++ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
String pdbIdStr = getResultTable().getValueAt(row,
- pdbIdColIndex)
- .toString();
+ pdbIdColIndex).toString();
SequenceI selectedSeq = (SequenceI) getResultTable()
- .getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
- }
- pdbEntriesToView[count++] = pdbEntry;
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- int[] selectedRows = tbl_local_pdb.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
+ }
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
- pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
++ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
+ row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
{
pdbEntry.setId(pdbIdStr);
}
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
- PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[] { selectedSequence });
- }
- else if (currentView == VIEWS_FROM_FILE)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE,
+ selectedSequence, true, Desktop.instance);
launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- sourceType);
- alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
++ alignFile = new JmolParser(inFile, sourceType);
}
else
{
--- /dev/null
+package jalview.io;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public enum FileFormat implements FileFormatI
+{
+ Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new FastaFile(inFile, sourceType);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new FastaFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new FastaFile();
+ }
+ },
+ Pfam("PFAM", "pfam", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new PfamFile(inFile, sourceType);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new PfamFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new PfamFile();
+ }
+ },
+ Stockholm("Stockholm", "sto,stk", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new StockholmFile(inFile, sourceType);
+ }
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new StockholmFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new StockholmFile(al);
+ }
+
+ },
+
+ PIR("PIR", "pir", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new PIRFile(inFile, sourceType);
+ }
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new PIRFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new PIRFile();
+ }
+ },
+ BLC("BLC", "BLC", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new BLCFile(inFile, sourceType);
+ } @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new BLCFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new BLCFile();
+ }
+ },
+ AMSA("AMSA", "amsa", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new AMSAFile(inFile, sourceType);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new AMSAFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new AMSAFile(al);
+ }
+ },
+ Html("HTML", "html", true, false)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new HtmlFile(inFile, sourceType);
+ } @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new HtmlFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new HtmlFile();
+ }
+
+ @Override
+ public boolean isComplexAlignFile()
+ {
+ return true;
+ }
+
+ },
+ Rnaml("RNAML", "xml,rnaml", true, false)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new RnamlFile(inFile, sourceType);
+ } @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new RnamlFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new RnamlFile();
+ }
+
+ },
+ Json("JSON","json", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new JSONFile(inFile, sourceType);
+ } @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new JSONFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new JSONFile();
+ }
+
+ @Override
+ public boolean isComplexAlignFile()
+ {
+ return true;
+ }
+
+ },
+ Pileup("PileUp", "pileup", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new PileUpfile(inFile, sourceType);
+ } @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new PileUpfile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new PileUpfile();
+ }
+
+ },
+ MSF("MSF", "msf", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new MSFfile(inFile, sourceType);
+ } @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new MSFfile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new MSFfile();
+ }
+
+ },
+ Clustal("Clustal", "aln", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new ClustalFile(inFile, sourceType);
+ } @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new ClustalFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new ClustalFile();
+ }
+ },
+ Phylip("PHYLIP", "phy", true, true)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new PhylipFile(inFile, sourceType);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new PhylipFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new PhylipFile();
+ }
+ },
+ Jnet("JnetFile", "", false, false)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ JPredFile af = new JPredFile(inFile, sourceType);
+ af.removeNonSequences();
+ return af;
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ JPredFile af = new JPredFile(source);
+ af.removeNonSequences();
+ return af;
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return null; // todo is this called?
+ }
+
+ },
+ Features("GFF or Jalview features", "gff2,gff3", true, false)
+ {
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return new FeaturesFile(true, inFile, sourceType);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return new FeaturesFile(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new FeaturesFile();
+ }
+ },
+ PDB("PDB", "pdb,ent", true, false)
+ {
+
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ // TODO obtain config value from preference settings.
+ // Set value to 'true' to test PDB processing with Jmol: JAL-1213
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
+ if (isParseWithJMOL)
+ {
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile,
- sourceType);
++ return new JmolParser(inFile, sourceType);
+ }
+ else
+ {
+ StructureImportSettings.setShowSeqFeatures(true);
+ return new MCview.PDBfile(
+ StructureImportSettings.isVisibleChainAnnotation(),
+ StructureImportSettings.isProcessSecondaryStructure(),
+ StructureImportSettings.isExternalSecondaryStructure(),
+ inFile,
+ sourceType);
+ }
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
+ if (isParseWithJMOL)
+ {
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
++ return new JmolParser(source);
+ }
+ else
+ {
+ StructureImportSettings.setShowSeqFeatures(true);
+ return new MCview.PDBfile(
+ StructureImportSettings.isVisibleChainAnnotation(),
+ StructureImportSettings.isProcessSecondaryStructure(),
+ StructureImportSettings.isExternalSecondaryStructure(),
+ source);
+ }
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new JmolParser(); // todo or null?
+ }
+ },
+ MMCif("mmCIF", "cif", true, false)
+ {
+
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile, sourceType);
++ return new JmolParser(inFile, sourceType);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
++ return new JmolParser(source);
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return new JmolParser(); // todo or null?
+ }
+ },
+ Jalview("Jalview", "jar,jvp", true, true)
+ {
+
+ @Override
+ public AlignmentFileI getAlignmentFile(String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ return null;
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(FileParse source)
+ throws IOException
+ {
+ return null;
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
+ {
+ return null;
+ }
+
+ @Override
+ public boolean isTextFormat()
+ {
+ return false;
+ }
+ };
+
+ /**
+ * A lookup map of enums by upper-cased name
+ */
+ private static Map<String, FileFormat> names;
+ static
+ {
+ names = new HashMap<String, FileFormat>();
+ for (FileFormat format : FileFormat.values())
+ {
+ names.put(format.toString().toUpperCase(), format);
+ }
+ }
+
+ private boolean writable;
+
+ private boolean readable;
+
+ private String extensions;
+
+ private String name;
+
+ /**
+ * Answers a list of writeable file formats (as string, corresponding to the
+ * toString() and forName() methods)
+ *
+ * @return
+ */
+ public static List<String> getWritableFormats(boolean textOnly)
+ {
+ List<String> l = new ArrayList<String>();
+ for (FileFormatI ff : values())
+ {
+ if (ff.isWritable() && (!textOnly || ff.isTextFormat()))
+ {
+ l.add(ff.toString());
+ }
+ }
+ return l;
+ }
+
+ /**
+ * Answers a list of readable file formats (as string, corresponding to the
+ * toString() and forName() methods)
+ *
+ * @return
+ */
+ public static List<String> getReadableFormats()
+ {
+ List<String> l = new ArrayList<String>();
+ for (FileFormatI ff : values())
+ {
+ if (ff.isReadable())
+ {
+ l.add(ff.toString());
+ }
+ }
+ return l;
+ }
+
+ @Override
+ public boolean isComplexAlignFile()
+ {
+ return false;
+ }
+
+ /**
+ * Returns the file format with the given name, or null if format is null or
+ * invalid. Unlike valueOf(), this is not case-sensitive, to be kind to
+ * writers of javascript.
+ *
+ * @param format
+ * @return
+ */
+ public static FileFormatI forName(String format)
+ {
+ // or could store format.getShortDescription().toUpperCase()
+ // in order to decouple 'given name' from enum name
+ return format == null ? null : names.get(format.toUpperCase());
+ }
+
+ @Override
+ public boolean isReadable()
+ {
+ return readable;
+ }
+
+ @Override
+ public boolean isWritable()
+ {
+ return writable;
+ }
+
+ /**
+ * Constructor
+ *
+ * @param shortName
+ * @param extensions
+ * comma-separated list of file extensions associated with the format
+ * @param isReadable
+ * @param isWritable
+ */
+ private FileFormat(String shortName, String extensions,
+ boolean isReadable, boolean isWritable)
+ {
+ this.name = shortName;
+ this.extensions = extensions;
+ this.readable = isReadable;
+ this.writable = isWritable;
+ }
+
+ @Override
+ public String getExtensions()
+ {
+ return extensions;
+ }
+
+ @Override
+ public String toString()
+ {
+ return name;
+ }
+
+ @Override
+ public AlignmentFileI getAlignmentFile()
+ {
+ return getAlignmentFile((AlignmentI) null);
+ }
+
+ @Override
+ public boolean isTextFormat()
+ {
+ return true;
+ }
+}
--/*
-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview is free software: you can redistribute it and/or
-- * modify it under the terms of the GNU General Public License
-- * as published by the Free Software Foundation, either version 3
-- * of the License, or (at your option) any later version.
-- *
-- * Jalview is distributed in the hope that it will be useful, but
-- * WITHOUT ANY WARRANTY; without even the implied warranty
-- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-- * PURPOSE. See the GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
-- */
package jalview.io;
- import jalview.bin.Cache;
- import jalview.datamodel.AlignmentI;
- import jalview.datamodel.SequenceI;
- import jalview.gui.AlignViewport;
+ import jalview.api.AlignExportSettingI;
+ import jalview.datamodel.AlignmentExportData;
+ import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignmentPanel;
- import jalview.gui.FeatureRenderer;
- import jalview.gui.SequenceRenderer;
- import jalview.util.BrowserLauncher;
- import jalview.util.ImageMaker;
+ import jalview.gui.IProgressIndicator;
import jalview.util.MessageManager;
- import java.awt.Color;
- import java.awt.Font;
- import java.io.FileWriter;
- import java.io.PrintWriter;
+ import java.io.BufferedReader;
+ import java.io.File;
+ import java.io.IOException;
+ import java.io.InputStreamReader;
+ import java.net.URL;
+ import java.util.Objects;
- public class HTMLOutput
-
+ public abstract class HTMLOutput implements Runnable
{
- AlignViewport av;
+ protected AlignmentPanel ap;
- SequenceRenderer sr;
+ protected long pSessionId;
- jalview.renderer.seqfeatures.FeatureRenderer fr;
+ protected IProgressIndicator pIndicator;
- Color color;
+ protected File generatedFile;
- public HTMLOutput(AlignmentPanel ap, SequenceRenderer sr,
- FeatureRenderer fr1)
+ public HTMLOutput(AlignmentPanel ap)
{
- this.av = ap.av;
- this.sr = sr;
-
- fr = new FeatureRenderer(ap);
- fr.transferSettings(fr1);
-
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), ImageMaker.HTML_EXTENSION,
- "HTML files", "HTML files");
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_as_html"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (ap != null)
{
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
-
- try
- {
- PrintWriter out = new PrintWriter(new FileWriter(choice));
- out.println("<HTML>");
- out.println("<style type=\"text/css\">");
- out.println("<!--");
- out.print("td {font-family: \"" + av.getFont().getFamily()
- + "\", \"" + av.getFont().getName() + "\", mono; "
- + "font-size: " + av.getFont().getSize() + "px; ");
-
- if (av.getFont().getStyle() == Font.BOLD)
- {
- out.print("font-weight: BOLD; ");
- }
-
- if (av.getFont().getStyle() == Font.ITALIC)
- {
- out.print("font-style: italic; ");
- }
-
- out.println("text-align: center; }");
-
- out.println("-->");
- out.println("</style>");
- out.println("<BODY>");
-
- if (av.getWrapAlignment())
- {
- drawWrappedAlignment(out);
- }
- else
- {
- drawUnwrappedAlignment(out);
- }
-
- out.println("\n</body>\n</html>");
- out.close();
- BrowserLauncher.openURL("file:///" + choice);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ this.ap = ap;
+ this.pIndicator = ap.alignFrame;
}
}
- void drawUnwrappedAlignment(PrintWriter out)
+ public String getBioJSONData()
{
- out.println("<table border=\"1\"><tr><td>\n");
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
-
- // ////////////
- SequenceI seq;
- AlignmentI alignment = av.getAlignment();
-
- // draws the top row, the measure rule
- out.println("<tr><td colspan=\"6\"></td>");
-
- int i = 0;
+ return getBioJSONData(null);
+ }
- for (i = 10; i < (alignment.getWidth() - 10); i += 10)
+ public String getBioJSONData(AlignExportSettingI exportSettings)
+ {
+ if (!isEmbedData())
{
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
+ return null;
}
-
- out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i
- + "<br>|</td>");
- out.println("</tr>");
-
- for (i = 0; i < alignment.getHeight(); i++)
+ if (exportSettings == null)
{
- seq = alignment.getSequenceAt(i);
-
- String id = seq.getDisplayId(av.getShowJVSuffix());
-
- out.println("<tr><td nowrap>" + id + " </td>");
-
- for (int res = 0; res < seq.getLength(); res++)
+ exportSettings = new AlignExportSettingI()
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+ @Override
+ public boolean isExportHiddenSequences()
{
- color = sr.getResidueBoxColour(seq, res);
+ return true;
+ }
- color = fr.findFeatureColour(color, seq, res);
+ @Override
+ public boolean isExportHiddenColumns()
+ {
+ return true;
}
- else
+
+ @Override
+ public boolean isExportAnnotations()
{
- color = Color.white;
+ return true;
}
- if (color.getRGB() < -1)
+ @Override
+ public boolean isExportFeatures()
{
- out.println("<td bgcolor=\"#"
- + jalview.util.Format.getHexString(color) + "\">"
- + seq.getCharAt(res) + "</td>");
+ return true;
}
- else
+
+ @Override
+ public boolean isExportGroups()
{
- out.println("<td>" + seq.getCharAt(res) + "</td>");
+ return true;
}
- }
- out.println("</tr>");
+ @Override
+ public boolean isCancelled()
+ {
+ return false;
+ }
+ };
}
-
- // ////////////
- out.println("</table>");
- out.println("</td></tr></table>");
+ AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(JSONFile.FILE_DESC,
++ .getAlignmentForExport(FileFormat.Json,
+ ap.getAlignViewport(), exportSettings);
+ String bioJSON = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC, exportData.getAlignment(),
++ .formatSequences(FileFormat.Json, exportData.getAlignment(),
+ exportData.getOmitHidden(), exportData
+ .getStartEndPostions(), ap.getAlignViewport()
+ .getColumnSelection());
+ return bioJSON;
}
- void drawWrappedAlignment(PrintWriter out)
+ /**
+ * Read a template file content as string
+ *
+ * @param file
+ * - the file to be read
+ * @return File content as String
+ * @throws IOException
+ */
+ public static String readFileAsString(File file) throws IOException
{
- // //////////////////////////////////
- // / How many sequences and residues can we fit on a printable page?
- AlignmentI al = av.getAlignment();
- SequenceI seq;
- String r;
- String g;
- String b;
-
- out.println("<table border=\"1\"><tr><td>\n");
- out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
-
- for (int startRes = 0; startRes < al.getWidth(); startRes += av
- .getWrappedWidth())
+ InputStreamReader isReader = null;
+ BufferedReader buffReader = null;
+ StringBuilder sb = new StringBuilder();
+ Objects.requireNonNull(file, "File must not be null!");
+ @SuppressWarnings("deprecation")
+ URL url = file.toURL();
+ if (url != null)
{
- int endRes = startRes + av.getWrappedWidth();
-
- if (endRes > al.getWidth())
- {
- endRes = al.getWidth();
- }
-
- if (av.getScaleAboveWrapped())
+ try
{
- out.println("<tr>");
-
- if (av.getScaleLeftWrapped())
+ isReader = new InputStreamReader(url.openStream());
+ buffReader = new BufferedReader(isReader);
+ String line;
+ String lineSeparator = System.getProperty("line.separator");
+ while ((line = buffReader.readLine()) != null)
{
- out.println("<td colspan=\"7\"> </td>");
+ sb.append(line).append(lineSeparator);
}
- else
- {
- out.println("<td colspan=\"6\"> </td>");
- }
-
- for (int i = startRes + 10; i < endRes; i += 10)
- {
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
- }
-
- out.println("</tr>");
- }
-
- int startPos, endPos;
- for (int s = 0; s < al.getHeight(); s++)
+
+ } catch (Exception ex)
{
- out.println("<tr>");
- seq = al.getSequenceAt(s);
-
- startPos = seq.findPosition(startRes);
- endPos = seq.findPosition(endRes) - 1;
-
- String id = seq.getDisplayId(av.getShowJVSuffix());
-
- out.println("<td nowrap>" + id + " </td>");
-
- if (av.getScaleLeftWrapped())
- {
- if (startPos > seq.getEnd() || endPos == 0)
- {
- out.println("<td nowrap> </td>");
- }
- else
- {
- out.println("<td nowrap>" + startPos + " </td>");
- }
- }
-
- for (int res = startRes; res < endRes; res++)
- {
- if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
- {
- color = sr.getResidueBoxColour(seq, res);
-
- color = fr.findFeatureColour(color, seq, res);
- }
- else
- {
- color = Color.white;
- }
-
- if (color.getRGB() < -1)
- {
- out.println("<td bgcolor=\"#"
- + jalview.util.Format.getHexString(color) + "\">"
- + seq.getCharAt(res) + "</td>");
- }
- else
- {
- out.println("<td>" + seq.getCharAt(res) + "</td>");
- }
-
- }
-
- if (av.getScaleRightWrapped()
- && endRes < startRes + av.getWrappedWidth())
+ ex.printStackTrace();
+ } finally
+ {
+ if (isReader != null)
{
- out.println("<td colspan=\""
- + (startRes + av.getWrappedWidth() - endRes) + "\">"
- + " </td>");
+ isReader.close();
}
-
- if (av.getScaleRightWrapped() && startPos < endPos)
+
+ if (buffReader != null)
{
- out.println("<td nowrap> " + endPos + " </td>");
+ buffReader.close();
}
-
- out.println("</tr>");
- }
-
- if (endRes < al.getWidth())
- {
- out.println("<tr><td height=\"5\"></td></tr>");
}
}
-
- out.println("</table>");
- out.println("</table>");
+ return sb.toString();
}
public static String getImageMapHTML()
+ "initToolTips(); //--></script>\n");
}
- }
+
+ public String getOutputFile() throws NoFileSelectedException
+ {
+ String selectedFile = null;
+ if (pIndicator != null && !isHeadless())
+ {
+ pIndicator.setProgressBar(MessageManager.formatMessage(
+ "status.waiting_for_user_to_select_output_file", "HTML"),
+ pSessionId);
+ }
+
+ JalviewFileChooser jvFileChooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" }, new String[] { "HTML files" },
+ "HTML files");
+ jvFileChooser.setFileView(new JalviewFileView());
+
+ jvFileChooser.setDialogTitle(MessageManager
+ .getString("label.save_as_html"));
+ jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int fileChooserOpt = jvFileChooser.showSaveDialog(null);
+ if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
+ .getSelectedFile().getParent());
+ selectedFile = jvFileChooser.getSelectedFile().getPath();
+ }
+ else
+ {
+ throw new NoFileSelectedException("No file was selected.");
+ }
+ return selectedFile;
+ }
+
+ protected void setProgressMessage(String message)
+ {
+ if (pIndicator != null && !isHeadless())
+ {
+ pIndicator.setProgressBar(message, pSessionId);
+ }
+ else
+ {
+ System.out.println(message);
+ }
+ }
+
+ /**
+ * Answers true if HTML export is invoke in headless mode or false otherwise
+ *
+ * @return
+ */
+ protected boolean isHeadless()
+ {
+ return System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true");
+ }
+
+ /**
+ * This method provides implementation of consistent behaviour which should
+ * occur before a HTML file export. It MUST be called at the start of the
+ * exportHTML() method implementation.
+ */
+ protected void exportStarted()
+ {
+ pSessionId = System.currentTimeMillis();
+ }
+
+ /**
+ * This method provides implementation of consistent behaviour which should
+ * occur after a HTML file export. It MUST be called at the end of the
+ * exportHTML() method implementation.
+ */
+ protected void exportCompleted()
+ {
+ if (isLaunchInBrowserAfterExport() && !isHeadless())
+ {
+ try
+ {
+ jalview.util.BrowserLauncher
+ .openURL("file:///" + getExportedFile());
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * if this answers true then BioJSON data will be embedded to the exported
+ * HTML file otherwise it won't be embedded.
+ *
+ * @return
+ */
+ public abstract boolean isEmbedData();
+
+ /**
+ * if this answers true then the generated HTML file is opened for viewing in
+ * a browser after its generation otherwise it won't be opened in a browser
+ *
+ * @return
+ */
+ public abstract boolean isLaunchInBrowserAfterExport();
+
+ /**
+ * handle to the generated HTML file
+ *
+ * @return
+ */
+ public abstract File getExportedFile();
+
+ /**
+ * This is the main method to handle the HTML generation.
+ *
+ * @param outputFile
+ * the file path of the generated HTML
+ */
+ public abstract void exportHTML(String outputFile);
-}
++}
alignSuffix.put("sto", "Stockholm File");
}
++ @Override
public String getTypeDescription(File f)
{
String extension = getExtension(f);
return type;
}
++ @Override
public Icon getIcon(File f)
{
String extension = getExtension(f);
private Vector<PDBChain> chains;
+ private boolean pdbIdAvailable;
+
- public StructureFile(String inFile, String type) throws IOException
+ public StructureFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public StructureFile(FileParse fp) throws IOException
Class cl = Class.forName("jalview.ext.jmol.JmolParser");
if (cl != null)
{
- final Constructor constructor = cl.getConstructor(new Class[] {
- boolean.class, boolean.class, boolean.class, FileParse.class });
- final Object[] args = new Object[] { visibleChainAnnotation,
- predictSecondaryStructure, externalSecondaryStructure,
- new FileParse(getDataName(), dataSourceType) };
- final Constructor constructor = cl
- .getConstructor(new Class[] { FileParse.class });
- final Object[] args = new Object[] { new FileParse(getDataName(),
- type) };
++ final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
++ final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
StructureImportSettings.setShowSeqFeatures(false);
StructureImportSettings.setVisibleChainAnnotation(false);
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType paste)
- String[] targetChains, String pdbFile, String protocol)
++ String[] targetChains, String pdbFile, DataSourceType protocol)
{
- return setMapping(true, sequence, targetChains, pdbFile, paste);
+ return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
-
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile,
- DataSourceType sourceType)
- String pdbFile, String protocol)
++ String pdbFile, DataSourceType sourceType)
{
/*
* There will be better ways of doing this in the future, for now we'll use
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
-
- boolean isParseWithJMOL = StructureImportSettings
- .getDefaultPDBFileParser().equalsIgnoreCase(
- StructureImportSettings.StructureParser.JMOL_PARSER
- .toString());
- if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
- {
- pdb = new JmolParser(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, sourceType);
- }
- else
- {
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, sourceType);
- }
- pdb = new JmolParser(pdbFile, protocol);
++ pdb = new JmolParser(pdbFile, sourceType);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && sourceType == DataSourceType.FILE)
- && AppletFormatAdapter.FILE.equals(protocol))
++ && DataSourceType.FILE == sourceType)
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
pdbFile = "INLINE" + pdb.getId();
}
-- ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
++ List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (isMapUsingSIFTs && seq.isProtein())
{
setProgressBar(null);
setProgressBar(MessageManager
}
else
{
-- ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
++ List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
for (PDBChain chain : pdb.getChains())
{
try
* @param pdbentry
* @param sequenceIs
* @param chains
- * @param protocol2
+ * @param protocol
*/
public AAStructureBindingModel(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- DataSourceType protocol2)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String protocol)
++ DataSourceType protocol)
{
this.ssm = ssm;
this.sequence = sequenceIs;
// retrieved.
startQuery();
AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
+ + queries.trim().toUpperCase(), DataSourceType.URL,
+ FileFormat.Stockholm);
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(DBRefSource.PFAM,
- // getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,
+ // getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase()));
if (!getDbSource().equals(DBRefSource.PFAM))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+ import jalview.structure.StructureImportSettings;
import java.io.IOException;
import java.util.List;
pf.addAnnotations(al);
return al.getAlignmentAnnotation();
}
+
- // @formatter:on
-
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ }
}
--- /dev/null
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+ package jalview.analysis;
+
+ import static org.testng.Assert.assertEquals;
+ import static org.testng.Assert.assertSame;
+ import static org.testng.Assert.assertTrue;
+
+ import jalview.datamodel.Alignment;
+ import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.SearchResultMatchI;
+ import jalview.datamodel.SearchResultsI;
+ import jalview.datamodel.Sequence;
+ import jalview.gui.AlignFrame;
++import jalview.io.DataSourceType;
+ import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+
+ import java.util.List;
+
+ import org.testng.annotations.BeforeClass;
+ import org.testng.annotations.Test;
+
+ public class FinderTest
+ {
+ private AlignFrame af;
+
+ private AlignmentI al;
+
+ @BeforeClass(groups = "Functional")
+ public void setUp()
+ {
+ String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n"
+ + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
+ af = new FileLoader().LoadFileWaitTillLoaded(seqData,
- FormatAdapter.PASTE);
++ DataSourceType.PASTE);
+ al = af.getViewport().getAlignment();
+ }
+
+ /**
+ * Test for find all matches of a regular expression
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_regex()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+ f.find("E.H"); // 'E, any character, H'
+
+ // should match seq2 efH and seq3 EFH
+ SearchResultsI sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 2);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
+ assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 7);
+ assertEquals(matches.get(1).getStart(), 4);
+ assertEquals(matches.get(1).getEnd(), 6);
+ }
+
+ /**
+ * Test for (undocumented) find residue by position
+ */
+ @Test(groups = "Functional")
+ public void testFind_residueNumber()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+ f.find("9");
+
+ // seq1 and seq4 have 9 residues; no match in other sequences
+ SearchResultsI sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 2);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
+ assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
+ assertEquals(matches.get(0).getStart(), 9);
+ assertEquals(matches.get(0).getEnd(), 9);
+ assertEquals(matches.get(1).getStart(), 9);
+ assertEquals(matches.get(1).getEnd(), 9);
+ }
+
+ /**
+ * Test for find next action
+ */
+ @Test(groups = "Functional")
+ public void testFindNext()
+ {
+ /*
+ * start at second sequence; resIndex of -1
+ * means sequence id / description is searched
+ */
+ Finder f = new Finder(al, null, 1, -1);
+ f.find("e"); // matches id
+
+ assertTrue(f.getSearchResults().isEmpty());
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
+
+ // resIndex is now 0 - for use in next find next
+ assertEquals(f.getResIndex(), 0);
+ f = new Finder(al, null, 1, 0);
+ f.find("e"); // matches in sequence
+ assertTrue(f.getIdMatch().isEmpty());
+ assertEquals(f.getSearchResults().getSize(), 1);
+ List<SearchResultMatchI> matches = f.getSearchResults().getResults();
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 5);
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
+ // still in the second sequence
+ assertEquals(f.getSeqIndex(), 1);
+ // next residue position to search from is 5
+ // (used as base 0 by RegEx so the same as 6 if base 1)
+ assertEquals(f.getResIndex(), 5);
+
+ // find next from end of sequence - finds next sequence id
+ f = new Finder(al, null, 1, 5);
+ f.find("e");
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al.getSequenceAt(2));
+ }
+
+ /**
+ * Test for matching within sequence descriptions
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_inDescription()
+ {
+ AlignmentI al2 = new Alignment(al);
+ al2.getSequenceAt(0).setDescription("BRAF");
+ al2.getSequenceAt(1).setDescription("braf");
+ Finder f = new Finder(al2, null);
+ f.setFindAll(true);
+ f.setIncludeDescription(true);
+
+ f.find("rAF");
+ assertEquals(f.getIdMatch().size(), 2);
+ assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+ assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * case sensitive
+ */
+ f = new Finder(al2, null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.setIncludeDescription(true);
+
+ f.find("RAF");
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * match sequence id, description and sequence!
+ */
+ al2.getSequenceAt(0).setDescription("the efh sequence");
+ al2.getSequenceAt(0).setName("mouseEFHkinase");
+ al2.getSequenceAt(1).setName("humanEFHkinase");
+ f = new Finder(al2, null);
+ f.setFindAll(true);
+ f.setIncludeDescription(true);
+
+ /*
+ * sequence matches should have no duplicates
+ */
+ f.find("EFH");
+ assertEquals(f.getIdMatch().size(), 2);
+ assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+ assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+
+ assertEquals(f.getSearchResults().getSize(), 2);
+ SearchResultMatchI match = f.getSearchResults().getResults().get(0);
+ assertSame(al2.getSequenceAt(1), match.getSequence());
+ assertEquals(5, match.getStart());
+ assertEquals(7, match.getEnd());
+ match = f.getSearchResults().getResults().get(1);
+ assertSame(al2.getSequenceAt(2), match.getSequence());
+ assertEquals(4, match.getStart());
+ assertEquals(6, match.getEnd());
+ }
+
+ /**
+ * Test for matching within sequence ids
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_sequenceIds()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+
+ /*
+ * case insensitive
+ */
+ f.find("SEQ1");
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al.getSequenceAt(0));
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * case sensitive
+ */
+ f = new Finder(al, null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.find("SEQ1");
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * match both sequence id and sequence
+ */
+ AlignmentI al2 = new Alignment(al);
+ al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
+ f = new Finder(al2, null);
+ f.setFindAll(true);
+ f.find("ABZ");
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4));
+ assertEquals(f.getSearchResults().getSize(), 2);
+ SearchResultMatchI match = f.getSearchResults().getResults().get(0);
+ assertSame(al2.getSequenceAt(4), match.getSequence());
+ assertEquals(4, match.getStart());
+ assertEquals(6, match.getEnd());
+ match = f.getSearchResults().getResults().get(1);
+ assertSame(al2.getSequenceAt(4), match.getSequence());
+ assertEquals(10, match.getStart());
+ assertEquals(12, match.getEnd());
+ }
+
+ /**
+ * Test finding all matches of a sequence pattern in an alignment
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_simpleMatch()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+
+ /*
+ * case insensitive first
+ */
+ f.find("EfH");
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(al.getSequenceAt(1), match.getSequence());
+ assertEquals(5, match.getStart());
+ assertEquals(7, match.getEnd());
+ match = searchResults.getResults().get(1);
+ assertSame(al.getSequenceAt(2), match.getSequence());
+ assertEquals(4, match.getStart());
+ assertEquals(6, match.getEnd());
+
+ /*
+ * case sensitive
+ */
+ f = new Finder(al, null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.find("BC");
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ match = searchResults.getResults().get(0);
+ assertSame(al.getSequenceAt(0), match.getSequence());
+ assertEquals(2, match.getStart());
+ assertEquals(3, match.getEnd());
+ match = searchResults.getResults().get(1);
+ assertSame(al.getSequenceAt(1), match.getSequence());
+ assertEquals(2, match.getStart());
+ assertEquals(3, match.getEnd());
+ }
+
+ /**
+ * Test for JAL-2302 to verify that sub-matches are not included in a find all
+ * result
+ */
+ @Test(groups = "Functional")
+ public void testFind_maximalResultOnly()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+ f.find("M+");
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(al.getSequenceAt(3), match.getSequence());
+ assertEquals(4, match.getStart()); // dataset sequence positions
+ assertEquals(8, match.getEnd()); // base 1
+ }
+ }
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+ import java.util.Arrays;
+
import org.testng.Assert;
import org.testng.annotations.Test;
+ "(" + s + ") should still be distinct from FER1_MAIZE (3)");
}
}
+
+ /**
+ * Check findFeatureAt doesn't return contact features except at contact
+ * points TODO:move to under the FeatureRendererModel test suite
+ */
+ @Test(groups = { "Functional" })
+ public void testFindFeatureAt_PointFeature() throws Exception
+ {
+ String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n"
+ + "c CCCCCCGGGGGGCCCCCC\n";
+ AlignFrame af = new jalview.io.FileLoader(false)
- .LoadFileWaitTillLoaded(alignment, FormatAdapter.PASTE);
++ .LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE);
+ SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
+ SequenceFeature sf = null;
+ sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
+ aseq.addSequenceFeature(sf);
+ Assert.assertTrue(sf.isContactFeature());
+ af.refreshFeatureUI(true);
+ af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
+ Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
+ .size(), 1, "Should be just one feature type displayed");
+ // step through and check for pointwise feature presence/absence
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1)
+ .size(), 0);
+ // step through and check for pointwise feature presence/absence
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2)
+ .size(), 1);
+ // step through and check for pointwise feature presence/absence
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3)
+ .size(), 0);
+ // step through and check for pointwise feature presence/absence
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4)
+ .size(), 0);
+ // step through and check for pointwise feature presence/absence
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5)
+ .size(), 1);
+ // step through and check for pointwise feature presence/absence
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6)
+ .size(), 0);
+ }
+
}
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+ import jalview.gui.AlignFrame;
++import jalview.io.DataSourceType;
+ import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+ import java.util.Arrays;
import java.util.BitSet;
import org.testng.annotations.Test;
assertEquals(0, seqCount);
assertEquals(0, bs.cardinality());
}
+
+ /**
+ * shameless copy of test data from findFeature for testing mark columns from
+ * highlight
+ */
+ @Test(groups = "Functional")
+ public void testSelectColumnsWithHighlight()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
+ + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
- + "seq4 aaaaaaaaaaaaaaaaaaaa\n", FormatAdapter.PASTE);
++ + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
+
+ SearchResultsI sr = new SearchResults();
+ SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+ SequenceI seq1 = sqs[0];
+ SequenceI seq2 = sqs[1];
+ SequenceI seq3 = sqs[2];
+ SequenceI seq4 = sqs[3];
+
+ /*
+ * features start/end are base 1
+ */
+ sr.addResult(seq1, 2, 4);
+ sr.addResult(seq2, 4, 10);
+ sr.addResult(seq3, 11, 15);
+
+ /*
+ * test Match/Find works first
+ */
+ Finder f = new Finder(af.getViewport().getAlignment(), null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.find("M+");
+ assertEquals(
+ "Finder found different set of results to manually created SearchResults",
+ sr, f.getSearchResults());
+
+ /*
+ * now check simple mark columns from find operation
+ */
+ af.getViewport().setSearchResults(sr);
+ AlignViewControllerI avc = af.avc;
+
+ avc.markHighlightedColumns(false, false, false);
+ assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
+ .getViewport().getColumnSelection().getSelectedRanges()
+ .toArray(), new int[][] { { 1, 14 } }));
+ }
}
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+ import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
}
@Test(dataProvider = "ens_seqs", suiteName = "live")
- public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
- throws Exception
+ public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
+ String fastasq) throws Exception
{
FileParse fp = proxy.getSequenceReader(Arrays
- .asList(new String[]
- { sq }));
+ .asList(new String[] { sq }));
SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
- FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
+ FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
SequenceI[] trueSqs = trueRes.getSeqsAsArray();
Assert.assertEquals(sqs.length, trueSqs.length,
"Different number of sequences retrieved for query " + sq);
for (String pdbStr : testFile)
{
PDBfile mctest = new PDBfile(false, false, false, pdbStr,
- AppletFormatAdapter.FILE);
- JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
- JmolParser jtest = new JmolParser(false, false, false, pdbStr,
- DataSourceType.FILE);
++ JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE);
Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
assertTrue(
public void testParse_missingResidues() throws Exception
{
PDBfile mctest = new PDBfile(false, false, false,
- pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
- JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
- AppletFormatAdapter.PASTE);
+ pastePDBDataWithChainBreak, DataSourceType.PASTE);
- boolean annotFromStructure = false;
- boolean localSecondaryStruct = false;
- boolean serviceSecondaryStruct = false;
- JmolParser jtest = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct,
- pastePDBDataWithChainBreak, DataSourceType.PASTE);
++ JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
public void testParse_alternativeResidues() throws Exception
{
PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
- AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
- boolean annotFromStructure = false;
- boolean localSecondaryStruct = false;
- boolean serviceSecondaryStruct = false;
- JmolParser jtest = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
+ JmolParser jtest = new JmolParser(pdbWithAltLoc,
- AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
-
+
assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
assertEquals("ALC", seqs.get(0).getSequenceAsString());
assertEquals('H', structCode[4]);
assertEquals('E', structCode[5]);
}
+
+ @Test(groups = "Functional")
+ public void testLocalPDBId() throws Exception
+ {
+ JmolParser structureData;
+ /*
+ * reads a local structure
+ */
+ structureData = new JmolParser("examples/testdata/localstruct.pdb",
- AppletFormatAdapter.FILE);
++ DataSourceType.FILE);
+ assertNotNull(structureData);
+ /*
+ * local structure files should yield a false ID based on the filename
+ */
+ assertNotNull(structureData.getId());
+ assertEquals(structureData.getId(), "localstruct.pdb");
+ assertNotNull(structureData.getSeqs());
+ /*
+ * the ID is also the group for features derived from structure data
+ */
+ assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
+ assertEquals(
+ structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
+ "localstruct.pdb");
+
+ }
}
JmolParser jtest = null;
try
{
-- mctest = new PDBfile(false, false, false, testFile,
- DataSourceType.FILE);
- jtest = new JmolParser(false, false, false, testFile,
- DataSourceType.FILE);
- AppletFormatAdapter.FILE);
- jtest = new JmolParser(testFile, AppletFormatAdapter.FILE);
++ mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE);
++ jtest = new JmolParser(testFile, DataSourceType.FILE);
} catch (IOException e)
{
System.err.println("Exception thrown while parsing : " + pdbStr);
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+ import jalview.bin.Cache;
+ import jalview.bin.Jalview;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
+ import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+ import jalview.datamodel.SearchResults;
+ import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+ import jalview.schemes.ColourSchemeI;
+ import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.MapList;
assertTrue(ssmMappings.contains(acf2));
assertFalse(ssmMappings.contains(acf3));
}
+
+ /**
+ * Test for JAL-1306 - conservation thread should run even when only Quality
+ * (and not Conservation) is enabled in Preferences
+ */
+ @Test(groups = { "Functional" })
+ public void testUpdateConservation_qualityOnly()
+ {
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.FALSE.toString());
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.FALSE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
++ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignmentAnnotation[] anns = af.viewport.getAlignment()
+ .getAlignmentAnnotation();
+ assertNotNull("No annotations found", anns);
+ assertEquals("More than one annotation found", 1, anns.length);
+ assertTrue("Annotation is not Quality",
+ anns[0].description.startsWith("Alignment Quality"));
+ Annotation[] annotations = anns[0].annotations;
+ assertNotNull("Quality annotations are null", annotations);
+ assertNotNull("Quality in column 1 is null", annotations[0]);
+ assertTrue("No quality value in column 1", annotations[0].value > 10f);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetGlobalColourScheme()
+ {
+ /*
+ * test for JAL-2283 don't inadvertently turn on colour by conservation
+ */
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.TRUE.toString());
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
++ "examples/uniref50.fa", DataSourceType.FILE);
+ ColourSchemeI cs = new PIDColourScheme();
+ af.getViewport().setGlobalColourScheme(cs);
+ assertFalse(cs.conservationApplied());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetGetHasSearchResults()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
++ "examples/uniref50.fa", DataSourceType.FILE);
+ SearchResultsI sr = new SearchResults();
+ SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+ // create arbitrary range on first sequence
+ sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
+
+ // test set
+ af.getViewport().setSearchResults(sr);
+ // has -> true
+ assertTrue(af.getViewport().hasSearchResults());
+ // get == original
+ assertEquals(sr, af.getViewport().getSearchResults());
+
+ // set(null) results in has -> false
+
+ af.getViewport().setSearchResults(null);
+ assertFalse(af.getViewport().hasSearchResults());
+ }
}
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+ import jalview.datamodel.DBRefEntry;
+ import jalview.datamodel.DBRefSource;
+ import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.util.MessageManager;
--- /dev/null
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+ package jalview.io;
+
+ import jalview.analysis.CrossRef;
+ import jalview.api.AlignmentViewPanel;
+ import jalview.datamodel.AlignedCodonFrame;
+ import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.AlignmentTest;
+ import jalview.datamodel.SequenceI;
+ import jalview.gui.AlignFrame;
+ import jalview.gui.CrossRefAction;
+ import jalview.gui.Desktop;
+ import jalview.gui.Jalview2XML;
+
+ import java.io.File;
+ import java.io.IOException;
+ import java.util.ArrayList;
+ import java.util.HashMap;
+ import java.util.List;
+
+ import org.testng.Assert;
+ import org.testng.annotations.Test;
+
+ @Test(singleThreaded = true)
+ public class CrossRef2xmlTests extends Jalview2xmlBase
+ {
+
+ /**
+ * test store and recovery of all reachable cross refs from all reachable
+ * crossrefs for one or more fetched db refs. Currently, this test has a known
+ * failure case.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Operational" }, enabled = true)
+ public void testRetrieveAndShowCrossref() throws Exception
+ {
+
+ List<String> failedDBRetr = new ArrayList<String>();
+ List<String> failedXrefMenuItems = new ArrayList<String>();
+ List<String> failedProjectRecoveries = new ArrayList<String>();
+
+ // for every set of db queries
+ // retrieve db query
+ // verify presence of expected xrefs
+ // show xrefs - verify expected type of frame is shown for each xref
+ // show xrefs again
+ // - verify original -> xref -> xref(original) recovers frame containing at
+ // least the first retrieved sequence
+ // store
+ // 1. whole project
+ // 2. individual frames
+ // 3. load each one back and verify
+ // . aligned sequences (.toString() )
+ // . xrefs (.toString() )
+ // . codonframes
+ //
+ //
+ HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
+ List<String> keyseq = new ArrayList<String>();
+ HashMap<String, File> savedProjects = new HashMap<String, File>();
+
+ for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
+ { "UNIPROT", "P01731" } })
+ {
+ // pass counters - 0 - first pass, 1 means retrieve project rather than
+ // perform action
+ int pass1 = 0, pass2 = 0, pass3 = 0;
+ // each do loop performs two iterations in the first outer loop pass, but
+ // only performs one iteration on the second outer loop
+ // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
+ // { pass 2 = 0 { pass 3 = 0 } }
+ do
+ {
+ String first = did[0] + " " + did[1];
+ AlignFrame af = null;
+ boolean dna;
+ AlignmentI retral;
+ AlignmentI dataset;
+ SequenceI[] seqs;
+ List<String> ptypes = null;
+ if (pass1 == 0)
+ {
+ // retrieve dbref
+
+ List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
+ did[0], did[1]);
+ if (afs.size() == 0)
+ {
+ failedDBRetr.add("Didn't retrieve " + first);
+ break;
+ }
+ keyseq.add(first);
+ af = afs.get(0);
+
+ // verify references for retrieved data
+ AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Fetch " + first + ":");
+ assertDatasetIsNormalisedKnownDefect(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Fetch " + first + ":");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
+
+ }
+ else
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ // recover stored project
+ af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
- .get(first).toString(), FormatAdapter.FILE);
++ .get(first).toString(), DataSourceType.FILE);
+ System.out.println("Recovered view for '" + first + "' from '"
+ + savedProjects.get(first).toString() + "'");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
+
+ // verify references for recovered data
+ AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Recover " + first + ":");
+ assertDatasetIsNormalisedKnownDefect(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Recover " + first + ":");
+
+ }
+
+ // store project on first pass, compare next pass
+ stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
+
+ ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
+ seqs, dataset).findXrefSourcesForSequences(dna);
+
+ // start of pass2: retrieve each cross-ref for fetched or restored
+ // project.
+ do // first cross ref and recover crossref loop
+ {
+
+ for (String db : ptypes)
+ {
+ // counter for splitframe views retrieved via crossref
+ int firstcr_ap = 0;
+ // build next key so we an retrieve all views
+ String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
+ // perform crossref action, or retrieve stored project
+ List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+ CrossRefAction cra = null;
+
+ if (pass2 == 0)
+ { // retrieve and show cross-refs in this thread
+ cra = new CrossRefAction(af, seqs, dna, db);
+ cra.run();
+ if (cra.getXrefViews().size() == 0)
+ {
+ failedXrefMenuItems.add("No crossrefs retrieved for "
+ + first + " -> " + db);
+ continue;
+ }
+ cra_views = cra.getXrefViews();
+ assertNucleotide(cra_views.get(0),
+ "Nucleotide panel included proteins for " + first
+ + " -> " + db);
+ assertProtein(cra_views.get(1),
+ "Protein panel included nucleotides for " + first
+ + " -> " + db);
+ }
+ else
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ pass3 = 0;
+ // recover stored project
+ File storedProject = savedProjects.get(nextxref);
+ if (storedProject == null)
+ {
+ failedProjectRecoveries.add("Failed to store a view for '"
+ + nextxref + "'");
+ continue;
+ }
+
+ // recover stored project
+ AlignFrame af2 = new FileLoader(false)
+ .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
- .toString(), FormatAdapter.FILE);
++ .toString(), DataSourceType.FILE);
+ System.out.println("Recovered view for '" + nextxref
+ + "' from '" + savedProjects.get(nextxref).toString()
+ + "'");
+ // gymnastics to recover the alignPanel/Complementary alignPanel
+ if (af2.getViewport().isNucleotide())
+ {
+ // top view, then bottom
+ cra_views.add(af2.getViewport().getAlignPanel());
+ cra_views.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+
+ }
+ else
+ {
+ // bottom view, then top
+ cra_views.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+ cra_views.add(af2.getViewport().getAlignPanel());
+
+ }
+ }
+ HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+ // first save/verify views.
+ for (AlignmentViewPanel avp : cra_views)
+ {
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ // verify references for this panel
+ AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
+ assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
+
+ SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
+
+ List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
+ : new CrossRef(xrseqs, dataset)
+ .findXrefSourcesForSequences(avp
+ .getAlignViewport().isNucleotide());
+
+ stringify(dbtoviewBit, savedProjects, nextxref, avp);
+ xrptypes.put(nextxref, _xrptypes);
+
+ }
+
+ // now do the second xref pass starting from either saved or just
+ // recovered split pane, in sequence
+ do // retrieve second set of cross refs or recover and verify
+ {
+ firstcr_ap = 0;
+ for (AlignmentViewPanel avp : cra_views)
+ {
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ for (String xrefdb : xrptypes.get(nextxref))
+ {
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+ int q = 0;
+ String nextnextxref = nextxref + " -> " + xrefdb + "{"
+ + q + "}";
+
+ if (pass3 == 0)
+ {
+
+ SequenceI[] xrseqs = avp.getAlignment()
+ .getSequencesArray();
+ AlignFrame nextaf = Desktop.getAlignFrameFor(avp
+ .getAlignViewport());
+
+ cra = new CrossRefAction(nextaf, xrseqs, avp
+ .getAlignViewport().isNucleotide(), xrefdb);
+ cra.run();
+ if (cra.getXrefViews().size() == 0)
+ {
+ failedXrefMenuItems
+ .add("No crossrefs retrieved for '"
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
+ continue;
+ }
+ cra_views2 = cra.getXrefViews();
+ assertNucleotide(cra_views2.get(0),
+ "Nucleotide panel included proteins for '"
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
+ assertProtein(cra_views2.get(1),
+ "Protein panel included nucleotides for '"
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
+
+ }
+ else
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ // recover stored project
+ File storedProject = savedProjects.get(nextnextxref);
+ if (storedProject == null)
+ {
+ failedProjectRecoveries
+ .add("Failed to store a view for '"
+ + nextnextxref + "'");
+ continue;
+ }
+ AlignFrame af2 = new FileLoader(false)
+ .LoadFileWaitTillLoaded(
+ savedProjects.get(nextnextxref)
- .toString(), FormatAdapter.FILE);
++ .toString(),
++ DataSourceType.FILE);
+ System.out.println("Recovered view for '"
+ + nextnextxref + "' from '"
+ + savedProjects.get(nextnextxref).toString()
+ + "'");
+ // gymnastics to recover the alignPanel/Complementary
+ // alignPanel
+ if (af2.getViewport().isNucleotide())
+ {
+ // top view, then bottom
+ cra_views2.add(af2.getViewport().getAlignPanel());
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+
+ }
+ else
+ {
+ // bottom view, then top
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+ cra_views2.add(af2.getViewport().getAlignPanel());
+ }
+ Assert.assertEquals(cra_views2.size(), 2);
+ Assert.assertNotNull(cra_views2.get(0));
+ Assert.assertNotNull(cra_views2.get(1));
+ }
+
+ for (AlignmentViewPanel nextavp : cra_views2)
+ {
+ nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
+ + "}";
+
+ // verify references for this panel
+ AlignmentTest.assertAlignmentDatasetRefs(
+ nextavp.getAlignment(), "" + "Pass (" + pass1
+ + "," + pass2 + "): For "
+ + nextnextxref + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ nextavp.getAlignment(), "" + "Pass (" + pass1
+ + "," + pass2 + "): For "
+ + nextnextxref + ":");
+
+ stringify(dbtoviewBit, savedProjects, nextnextxref,
+ nextavp);
+ keyseq.add(nextnextxref);
+ }
+ } // end of loop around showing all xrefdb for crossrf2
+
+ } // end of loop around all viewpanels from crossrf1
+ } while (pass2 == 2 && pass3++ < 2);
+ // fetchdb->crossref1->crossref-2->verify for xrefs we
+ // either loop twice when pass2=0, or just once when pass2=1
+ // (recovered project from previous crossref)
+
+ } // end of loop over db-xrefs for crossref-2
+
+ // fetchdb-->crossref1
+ // for each xref we try to retrieve xref, store and verify when
+ // pass1=0, or just retrieve and verify when pass1=1
+ } while (pass1 == 1 && pass2++ < 2);
+ // fetchdb
+ // for each ref we
+ // loop twice: first, do the retrieve, second recover from saved project
+
+ // increment pass counters, so we repeat traversal starting from the
+ // oldest saved project first.
+ if (pass1 == 0)
+ {
+ // verify stored projects for first set of cross references
+ pass1 = 1;
+ // and verify cross-references retrieved from stored projects
+ pass2 = 0;
+ pass3 = 0;
+ }
+ else
+ {
+ pass1++;
+ }
+ } while (pass1 < 3);
+ }
+ if (failedXrefMenuItems.size() > 0)
+ {
+ for (String s : failedXrefMenuItems)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
+ + " counts)");
+ }
+ if (failedProjectRecoveries.size() > 0)
+ {
+
+ for (String s : failedProjectRecoveries)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
+ + failedProjectRecoveries.size() + " counts)");
+ }
+ if (failedDBRetr.size() > 0)
+ {
+ for (String s : failedProjectRecoveries)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
+ + failedDBRetr.size() + " counts)");
+ }
+ }
+
+ /**
+ * wrapper to trap known defect for AH002001 testcase
+ *
+ * @param alignment
+ * @param string
+ */
+ private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
+ String message)
+ {
+ try
+ {
+ AlignmentTest.assertDatasetIsNormalised(al, message);
+ } catch (AssertionError ae)
+ {
+ if (!ae.getMessage().endsWith("EMBL|AH002001"))
+ {
+ throw ae;
+ }
+ else
+ {
+ System.out
+ .println("Ignored exception for known defect: JAL-2179 : "
+ + message);
+ }
+
+ }
+ }
+
+ private void assertProtein(AlignmentViewPanel alignmentViewPanel,
+ String message)
+ {
+ assertType(true, alignmentViewPanel, message);
+ }
+
+ private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
+ String message)
+ {
+ assertType(false, alignmentViewPanel, message);
+ }
+
+ private void assertType(boolean expectProtein,
+ AlignmentViewPanel alignmentViewPanel, String message)
+ {
+ List<SequenceI> nonType = new ArrayList<SequenceI>();
+ for (SequenceI sq : alignmentViewPanel.getAlignViewport()
+ .getAlignment().getSequences())
+ {
+ if (sq.isProtein() != expectProtein)
+ {
+ nonType.add(sq);
+ }
+ }
+ if (nonType.size() > 0)
+ {
+ Assert.fail(message + " [ "
+ + (expectProtein ? "nucleotides were " : "proteins were ")
+ + nonType.toString() + " ]");
+ }
+ }
+
+ /**
+ * first time called, record strings derived from alignment and
+ * alignedcodonframes, and save view to a project file. Second time called,
+ * compare strings to existing ones. org.testng.Assert.assertTrue on
+ * stringmatch
+ *
+ * @param dbtoviewBit
+ * map between xrefpath and view string
+ * @param savedProjects
+ * - map from xrefpath to saved project filename (createTempFile)
+ * @param xrefpath
+ * - xrefpath - unique ID for this context (composed of sequence of
+ * db-fetch/cross-ref actions preceeding state)
+ * @param avp
+ * - viewpanel to store (for viewpanels in splitframe, the same
+ * project should be written for both panels, only one needs
+ * recovering for comparison on the next stringify call, but each
+ * viewpanel needs to be called with a distinct xrefpath to ensure
+ * each one's strings are compared)
+ */
+ private void stringify(HashMap<String, String> dbtoviewBit,
+ HashMap<String, File> savedProjects, String xrefpath,
+ AlignmentViewPanel avp)
+ {
+ if (savedProjects != null)
+ {
+ if (savedProjects.get(xrefpath) == null)
+ {
+ // write a project file for this view. On the second pass, this will be
+ // recovered and cross-references verified
+ try
+ {
+ File prfile = File.createTempFile("crossRefTest", ".jvp");
+ AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
+ new Jalview2XML(false).saveAlignment(af, prfile.toString(),
+ af.getTitle());
+ System.out.println("Written view from '" + xrefpath + "' as '"
+ + prfile.getAbsolutePath() + "'");
+ savedProjects.put(xrefpath, prfile);
+ } catch (IOException q)
+ {
+ Assert.fail("Unexpected IO Exception", q);
+ }
+ }
+ else
+ {
+ System.out.println("Stringify check on view from '" + xrefpath
+ + "' [ possibly retrieved from '"
+ + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
+
+ }
+ }
+
+ StringBuilder sbr = new StringBuilder();
+ sbr.append(avp.getAlignment().toString());
+ sbr.append("\n");
+ sbr.append("<End of alignment>");
+ sbr.append("\n");
+ sbr.append(avp.getAlignment().getDataset());
+ sbr.append("\n");
+ sbr.append("<End of dataset>");
+ sbr.append("\n");
+ int p = 0;
+ if (avp.getAlignment().getCodonFrames() != null)
+ {
+ for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
+ {
+ sbr.append("<AlignedCodonFrame " + p++ + ">");
+ sbr.append("\n");
+ sbr.append(ac.toString());
+ sbr.append("\n");
+ }
+ }
+ String dbt = dbtoviewBit.get(xrefpath);
+ if (dbt == null)
+ {
+ dbtoviewBit.put(xrefpath, sbr.toString());
+ }
+ else
+ {
+ Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "
+ + xrefpath);
+ }
+ }
+ }
String inFile = "examples/RF00031_folded.stk";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
- FormatAdapter.FILE);
- assertNotNull("Didn't read input file " + inFile, af);
++ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ inFile, DataSourceType.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
int olddsann = countDsAnn(af.getViewport());
assertTrue("Didn't find any dataset annotations", olddsann > 0);
af.rnahelicesColour_actionPerformed(null);
"Couldn't apply RNA helices colourscheme",
af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
+ af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- DataSourceType.FILE);
- af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
- assertNotNull("Failed to import new project", af);
++ af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ assertTrue("Failed to import new project", af != null);
int newdsann = countDsAnn(af.getViewport());
assertTrue(
"Differing numbers of dataset sequence annotation\nOriginally "
String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
- FormatAdapter.FILE);
++ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ inFile, DataSourceType.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
+ assertNotNull("Didn't read input file " + inFile, af);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- assertTrue(
- "Didn't set T-coffee colourscheme",
- af.getViewport().getGlobalColourScheme().getClass()
- .equals(jalview.schemes.TCoffeeColourScheme.class));
- assertTrue(
- "Recognise T-Coffee score from string",
- jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
- .getAlignment(),
- jalview.schemes.ColourSchemeProperty.getColourName(af
- .getViewport().getGlobalColourScheme())) != null);
+ assertSame("Didn't set T-coffee colourscheme", af.getViewport()
+ .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
+ assertNotNull("Recognise T-Coffee score from string",
- jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
++ ColourSchemeProperty.getColour(af.getViewport()
+ .getAlignment(), ColourSchemeProperty.getColourName(af
+ .getViewport().getGlobalColourScheme())));
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
+ af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
++ af = new FileLoader().LoadFileWaitTillLoaded(tfile,
+ DataSourceType.FILE);
- assertTrue("Failed to import new project", af != null);
- assertTrue(
- "Didn't set T-coffee colourscheme for imported project.",
- af.getViewport().getGlobalColourScheme().getClass()
- .equals(jalview.schemes.TCoffeeColourScheme.class));
+ assertNotNull("Failed to import new project", af);
+ assertSame("Didn't set T-coffee colourscheme for imported project.", af
+ .getViewport().getGlobalColourScheme().getClass(),
+ TCoffeeColourScheme.class);
System.out
.println("T-Coffee score shading successfully recovered from project.");
}
String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, DataSourceType.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
- FormatAdapter.FILE);
++ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
+ assertNotNull("Didn't read input file " + inFile, af);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
AlignmentAnnotation[] aa = af.getViewport().getAlignment()
.getSequenceAt(0).getAnnotation("IUPredWS (Short)");
assertTrue(
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
af.alignPanel.alignmentChanged();
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
+ af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- DataSourceType.FILE);
- af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
- assertNotNull("Failed to import new project", af);
++ af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+ assertTrue("Failed to import new project", af != null);
// check for group and alignment colourschemes
{
int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
.getAlignFrames().length;
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
+ assertNotNull("Didn't read in the example file correctly.", af);
assertTrue("Didn't gather the views in the example file.",
Desktop.getAlignFrames().length == 1 + origCount);
@Test(groups = { "Functional" })
public void viewRefPdbAnnotation() throws Exception
{
- // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER
- // StructureImportSettings
- // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
StructureImportSettings.setProcessSecondaryStructure(true);
StructureImportSettings.setVisibleChainAnnotation(true);
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
+ assertNotNull("Didn't read in the example file correctly.", af);
AlignmentViewPanel sps = null;
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
{
@Test(groups = { "Functional" })
public void testCopyViewSettings() throws Exception
{
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
+ assertNotNull("Didn't read in the example file correctly.", af);
AlignmentViewPanel sps = null, groups = null;
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
{
{
Desktop.instance.closeAll_actionPerformed(null);
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
Assert.assertEquals(Desktop.getAlignFrames().length, 1);
String afid = af.getViewport().getSequenceSetId();
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
}
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
- FormatAdapter.FILE);
++ af = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), DataSourceType.FILE);
Assert.assertNotNull(af);
Assert.assertEquals(
Desktop.getAlignFrames().length,
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
+ assertNotNull("Didn't read in the example file correctly.", af);
String afid = af.getViewport().getSequenceSetId();
// remember reference sequence for each panel
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
+ "examples/uniref50.fa", DataSourceType.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
+ assertNotNull("Didn't read in the example file correctly.", af);
String afid = af.getViewport().getSequenceSetId();
// make a second view of the alignment
af.newView_actionPerformed(null);
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
}
-
- af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
- FormatAdapter.FILE);
+
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), DataSourceType.FILE);
afid = af.getViewport().getSequenceSetId();
-
+
for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
{
String viewName = ap.getViewName();
Desktop.instance.closeAll_actionPerformed(null);
String exampleFile = "examples/3W5V.pdb";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
+ assertNotNull("Didn't read in the example file correctly.", af);
String afid = af.getViewport().getSequenceSetId();
AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
public class PfamFormatInputTest
{
- @Test
+ @Test(groups = "Functional")
public void testPfamFormatNoLimits() throws IOException
{
- AlignmentI al = new jalview.io.AppletFormatAdapter().readFile("ASEQ"
+ AlignmentI al = new AppletFormatAdapter().readFile("ASEQ"
- + '\t' + "...--FFAFAFF--", AppletFormatAdapter.PASTE, "PFAM");
+ + '\t' + "...--FFAFAFF--", DataSourceType.PASTE,
+ FileFormat.Pfam);
Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
Assert.assertTrue(al.hasValidSequence(),
"Didn't extract limits from PFAM ID");
}
- @Test
+ @Test(groups = "Functional")
public void testPfamFormatValidLimits() throws IOException
{
- AlignmentI al = new jalview.io.AppletFormatAdapter().readFile(
- "ASEQ/15-25" + '\t' + "...--FFAFAFF--",
- DataSourceType.PASTE,
- FileFormat.Pfam);
- AlignmentI al = new AppletFormatAdapter().readFile(
- "ASEQ/15-25" + '\t' + "...--FFAFAFF--",
- AppletFormatAdapter.PASTE, "PFAM");
++ AlignmentI al = new AppletFormatAdapter().readFile("ASEQ/15-25" + '\t'
++ + "...--FFAFAFF--", DataSourceType.PASTE, FileFormat.Pfam);
Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
Assert.assertTrue(al.hasValidSequence(),
"Didn't extract limits from PFAM ID");
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
- jalview.io.DataSourceType.FILE);
- jalview.io.FormatAdapter.FILE);
++ DataSourceType.FILE);
assertTrue(pmap != null);
SequenceI protseq = pmap.getSeqsAsArray()[0];
AlignmentAnnotation pstra = protseq
// Associate the 1GAQ pdb file with the subsequence 'imported' from another
// source
StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
- new String[] { "A" }, inFile = "examples/1gaq.txt",
- jalview.io.FormatAdapter.FILE);
+ new String[]
- { "A" }, inFile = "examples/1gaq.txt", jalview.io.DataSourceType.FILE);
++ { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
assertTrue("PDB File couldn't be found", pde != null);
StructureMapping[] mp = ssm.getMapping(inFile);
assertTrue("No mappings made.", mp != null && mp.length > 0);
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
new String[] { null }, "examples/3W5V.pdb",
- jalview.io.DataSourceType.FILE);
- jalview.io.FormatAdapter.FILE);
++ DataSourceType.FILE);
if (pmap == null)
{
AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
StructureImportSettings.setShowSeqFeatures(true);
AlignFrame ref = new FileLoader(false)
.LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
- jalview.io.DataSourceType.FILE);
- jalview.io.FormatAdapter.FILE);
++ DataSourceType.FILE);
SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
SequenceI newseq = new Sequence(refseq.getName() + "Copy",
refseq.getSequenceAsString());
ssm.setAddTempFacAnnot(true);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
- jalview.io.DataSourceType.FILE);
- jalview.io.FormatAdapter.FILE);
++ DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals("Original and copied sequence of different lengths.",
refseq.getLength(), newseq.getLength());
seqs[2] = new SequenceI[] { seq3 };
StructureSelectionManager ssm = new StructureSelectionManager();
- ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
+ ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
- AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
- AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
- AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
- testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
+ testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
{
@Override
public String[] getPdbFile()
Assert.assertEquals(entityD.getEntityId(), "D");
}
+
+ @Test(groups = { "Functional" })
+ public void getEntityByMostOptimalMatchedIdTest2()
+ {
+ // This test is for a SIFTS file in which entity A should map to chain P for
+ // the given PDB Id. All the other chains shouldn't be mapped as there are
+ // no SIFTS entity records for them.
+ SiftsClient siftsClientX = null;
+ PDBfile pdbFile;
+ try
+ {
+ pdbFile = new PDBfile(false, false, false,
- "test/jalview/io/3ucu.cif", AppletFormatAdapter.FILE);
++ "test/jalview/io/3ucu.cif", DataSourceType.FILE);
+ siftsClientX = new SiftsClient(pdbFile);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
+ Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
+ Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
+ Assert.assertEquals(entityA.getEntityId(), "A");
+ Assert.assertNotEquals(entityR, "A");
+ Assert.assertNotEquals(entityP, "A");
+ Assert.assertNotEquals(entityR, "R");
+ Assert.assertNotEquals(entityP, "P");
+ Assert.assertNull(entityR);
+ Assert.assertNull(entityP);
+
+ }
}
git://source.jalview.org / jalview.git / commitdiff