package jalview.bin;
import java.io.File;
+import java.io.IOException;
+import java.util.AbstractMap;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.Map.Entry;
import jalview.analysis.AlignmentUtils;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubVal;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.ArgValue;
+import jalview.bin.argparser.ArgValues;
+import jalview.bin.argparser.ArgValuesMap;
+import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
+import jalview.gui.AssociatePdbFileWithSeq;
import jalview.gui.Desktop;
+import jalview.gui.Preferences;
import jalview.gui.StructureChooser;
+import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
-import jalview.structure.StructureImportSettings;
+import jalview.schemes.AnnotationColourGradient;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
+import mc_view.PDBChain;
public class Commands
{
Desktop desktop;
- private static boolean headless;
+ private boolean headless;
- private static ArgParser argParser;
+ private ArgParser argParser;
private Map<String, AlignFrame> afMap;
- public static void processArgs(ArgParser ap, boolean h)
+ private boolean commandArgsProvided = false;
+
+ private boolean argsWereParsed = false;
+
+ public Commands(ArgParser argparser, boolean headless)
{
- argParser = ap;
- headless = h;
+ this(Desktop.instance, argparser, headless);
+ }
- if (headless)
+ public Commands(Desktop d, ArgParser argparser, boolean h)
+ {
+ argParser = argparser;
+ headless = h;
+ desktop = d;
+ afMap = new HashMap<String, AlignFrame>();
+ if (argparser != null)
{
- System.setProperty("java.awt.headless", "true");
+ processArgs(argparser, headless);
}
+ }
+
+ private boolean processArgs(ArgParser argparser, boolean h)
+ {
+ argParser = argparser;
+ headless = h;
+ boolean theseArgsWereParsed = false;
if (argParser != null && argParser.linkedIds() != null)
{
for (String id : argParser.linkedIds())
{
- Console.debug("##### id=" + id);
- Commands cmds = new Commands();
+ ArgValuesMap avm = argParser.linkedArgs(id);
+ theseArgsWereParsed = true;
if (id == null)
{
- cmds.processUnlinked(id);
+ theseArgsWereParsed &= processUnlinked(id);
}
else
{
- cmds.processLinked(id);
+ theseArgsWereParsed &= processLinked(id);
}
- cmds.processImages(id);
+ theseArgsWereParsed &= processImages(id);
+
+ // close ap
+ if (avm.getBoolean(Arg.CLOSE))
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.closeMenuItem_actionPerformed(true);
+ }
+ }
+
}
}
if (argParser.getBool(Arg.QUIT))
{
Jalview.getInstance().quit();
- // Desktop.instance.quit();
+ return true;
}
+ // carry on with jalview.bin.Jalview
+ argsWereParsed = theseArgsWereParsed;
+ return argsWereParsed;
}
- public Commands()
+ public boolean commandArgsProvided()
{
- this(Desktop.instance);
+ return commandArgsProvided;
}
- public Commands(Desktop d)
+ public boolean argsWereParsed()
{
- this.desktop = d;
- afMap = new HashMap<String, AlignFrame>();
+ return argsWereParsed;
}
- protected void processUnlinked(String id)
+ protected boolean processUnlinked(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
-
- processLinked(id);
+ return processLinked(id);
}
- protected void processLinked(String id)
+ protected boolean processLinked(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ boolean theseArgsWereParsed = false;
+ ArgValuesMap avm = argParser.linkedArgs(id);
+ if (avm == null)
+ return true;
/*
- // script to execute after all loading is completed one way or another
- String groovyscript = m.get(Arg.GROOVY) == null ? null
- : m.get(Arg.GROOVY).getValue();
- String file = m.get(Arg.OPEN) == null ? null
- : m.get(Arg.OPEN).getValue();
- String data = null;
- FileFormatI format = null;
- DataSourceType protocol = null;
- */
- if (ArgParser.getArgValues(m, Arg.OPEN) != null)
+ * // script to execute after all loading is completed one way or another String
+ * groovyscript = m.get(Arg.GROOVY) == null ? null :
+ * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
+ * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
+ * DataSourceType protocol = null;
+ */
+ if (avm.containsArg(Arg.OPEN) || avm.containsArg(Arg.OPENNEW))
{
+ commandArgsProvided = true;
long progress = -1;
boolean first = true;
+ boolean progressBarSet = false;
AlignFrame af;
- OPEN: for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+ // Combine the OPEN and OPENNEW files into one list, along with whether it
+ // was OPEN or OPENNEW
+ List<Entry<Arg, ArgValue>> openAvList = new ArrayList<>();
+ avm.getArgValueList(Arg.OPEN).stream()
+ .forEachOrdered(av -> openAvList.add(
+ new AbstractMap.SimpleEntry<Arg, ArgValue>(Arg.OPEN,
+ av)));
+ avm.getArgValueList(Arg.OPENNEW).stream()
+ .forEachOrdered(av -> openAvList
+ .add(new AbstractMap.SimpleEntry<Arg, ArgValue>(
+ Arg.OPENNEW, av)));
+ for (Entry<Arg, ArgValue> aav : openAvList)
{
+ Arg a = aav.getKey();
+ ArgValue av = aav.getValue();
+ String openFile = av.getValue();
if (openFile == null)
- continue OPEN;
+ continue;
+ theseArgsWereParsed = true;
if (first)
{
first = false;
- if (!headless)
+ if (!headless && desktop != null)
{
desktop.setProgressBar(
MessageManager.getString(
"status.processing_commandline_args"),
progress = System.currentTimeMillis());
+ progressBarSet = true;
}
}
if (!(new File(openFile)).exists())
{
Console.warn("Can't find file '" + openFile + "'");
- continue OPEN;
}
}
}
}
af = afMap.get(id);
- if (af == null)
+ if (af == null || "true".equals(av.getSubVal("new"))
+ || a == Arg.OPENNEW || format == FileFormat.Jalview)
{
/*
- * this approach isn't working yet
- // get default annotations before opening AlignFrame
- if (m.get(Arg.SSANNOTATION) != null)
- {
- Console.debug("***** SSANNOTATION="
- + m.get(Arg.SSANNOTATION).getBoolean());
- }
- if (m.get(Arg.NOTEMPFAC) != null)
- {
- Console.debug(
- "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
- }
- boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
- ? m.get(Arg.SSANNOTATION).getBoolean()
- : false;
- boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
- ? !m.get(Arg.NOTEMPFAC).getBoolean()
- : false;
- Console.debug("***** tempfac=" + showTemperatureFactor
- + ", showSS=" + showSecondaryStructure);
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (ssm != null)
- {
- ssm.setAddTempFacAnnot(showTemperatureFactor);
- ssm.setProcessSecondaryStructure(showSecondaryStructure);
- }
+ * this approach isn't working yet // get default annotations before opening
+ * AlignFrame if (m.get(Arg.SSANNOTATION) != null) {
+ * Console.debug("##### SSANNOTATION=" + m.get(Arg.SSANNOTATION).getBoolean());
+ * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
+ * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
+ * (m.get(Arg.SSANNOTATION) != null) ? m.get(Arg.SSANNOTATION).getBoolean() :
+ * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
+ * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
+ * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
+ * StructureSelectionManager ssm = StructureSelectionManager
+ * .getStructureSelectionManager(Desktop.instance); if (ssm != null) {
+ * ssm.setAddTempFacAnnot(showTemperatureFactor);
+ * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
*/
- // get kind of temperature factor annotation
- StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
- if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
- && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
- {
- try
- {
- tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
- .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
- Console.debug("Obtained Temperature Factor type of '"
- + tempfacType + "'");
- } catch (IllegalArgumentException e)
- {
- // Just an error message!
- StringBuilder sb = new StringBuilder().append("Cannot set --")
- .append(Arg.TEMPFAC.getName()).append(" to '")
- .append(tempfacType)
- .append("', ignoring. Valid values are: ");
- Iterator<StructureImportSettings.TFType> it = Arrays
- .stream(StructureImportSettings.TFType.values())
- .iterator();
- while (it.hasNext())
- {
- sb.append(it.next().toString().toLowerCase(Locale.ROOT));
- if (it.hasNext())
- sb.append(", ");
- }
- Console.warn(sb.toString());
- }
- }
-
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
- StructureImportSettings.setTemperatureFactorType(tempfacType);
-
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
// wrap alignment?
- if (ArgParser.getBoolean(m, Arg.WRAP))
+ if (avm.getBoolean(Arg.WRAP))
{
af.getCurrentView().setWrapAlignment(true);
}
+ // colour aligment?
+ if (avm.containsArg(Arg.COLOUR))
+ {
+ af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+ }
+
// change alignment frame title
- if (ArgParser.getValue(m, Arg.TITLE) != null)
- af.setTitle(ArgParser.getValue(m, Arg.TITLE));
+ if (avm.containsArg(Arg.TITLE))
+ af.setTitle(avm.getValue(Arg.TITLE));
/* hacky approach to hiding the annotations */
// show secondary structure annotations?
- if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
+ if (avm.getBoolean(Arg.SSANNOTATION))
{
// do this better (annotation types?)
AlignmentUtils.showOrHideSequenceAnnotations(
}
// show temperature factor annotations?
- if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+ if (avm.getBoolean(Arg.NOTEMPFAC))
{
// do this better (annotation types?)
List<String> hideThese = new ArrayList<>();
false, false);
}
else
- /* comment out hacky approach up to here and add this line:
- if (showTemperatureFactor)
- */
+ /*
+ * comment out hacky approach up to here and add this line: if
+ * (showTemperatureFactor)
+ */
{
- if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
+ if (avm.containsArg(Arg.TEMPFAC_LABEL))
{
AlignmentAnnotation aa = AlignmentUtils
.getFirstSequenceAnnotationOfType(
af.getCurrentView().getAlignment(),
AlignmentAnnotation.LINE_GRAPH);
- String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
+ String label = avm.getValue(Arg.TEMPFAC_LABEL);
if (aa != null)
{
aa.label = label;
.getStructureSelectionManager(Desktop.instance);
SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
ssm.computeMapping(false, new SequenceI[] { seq }, null,
- openFile, DataSourceType.FILE, null);
+ openFile, DataSourceType.FILE, null, null, null);
}
}
else
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
- af.getCurrentView().addFile(new File(openFile), format);
+ af.getCurrentView().addFile(new File(openFile), format, false);
}
- System.out
- .println("Command " + Arg.OPEN + " executed successfully!");
+ Console.debug("Command " + Arg.OPEN + " executed successfully!");
}
if (first) // first=true means nothing opened
{
if (headless)
{
- Console.error("Could not open any files in headless mode");
- System.exit(1);
+ Jalview.exit("Could not open any files in headless mode", 1);
+ }
+ else
+ {
+ Console.warn("No more files to open");
}
}
- else
- {
- Console.warn("No more files to open");
- if (desktop != null)
- desktop.setProgressBar(null, progress);
- }
+ if (progressBarSet && desktop != null)
+ desktop.setProgressBar(null, progress);
}
- // load a pAE file if given
- if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
+ // open the structure (from same PDB file or given PDBfile)
+ if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
AlignFrame af = afMap.get(id);
- if (af != null)
+ if (avm.containsArg(Arg.STRUCTURE))
{
- for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
+ commandArgsProvided = true;
+ for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
- SubVal subVal = ArgParser.getSubVal(val);
- File paeFile = new File(subVal.content);
- String structId = "structid".equals(subVal.keyName)
- ? subVal.keyValue
- : null;
- if (subVal.notSet())
- {
- // take structid from pdbfilename
- }
- if ("structfile".equals(subVal.keyName))
- {
- EBIAlfaFold.addAlphaFoldPAEToStructure(
- af.getCurrentView().getAlignment(), paeFile,
- subVal.index, subVal.keyValue, false);
- }
- else if ("structid".equals(subVal.keyName))
- {
- EBIAlfaFold.addAlphaFoldPAEToStructure(
- af.getCurrentView().getAlignment(), paeFile,
- subVal.index, subVal.keyValue, true);
- }
- else
- {
- EBIAlfaFold.addAlphaFoldPAEToSequence(
- af.getCurrentView().getAlignment(), paeFile,
- subVal.index,
- "seqid".equals(subVal.keyName) ? subVal.keyValue
- : null);
- // required to readjust the height and position of the pAE
- // annotation
- }
- for (AlignmentViewPanel ap : af.getAlignPanels())
+ String val = av.getValue();
+ SubVals subVals = av.getSubVals();
+ SequenceI seq = getSpecifiedSequence(af, subVals);
+ if (seq == null)
{
- ap.adjustAnnotationHeight();
+ // Could not find sequence from subId, let's assume the first
+ // sequence in the alignframe
+ AlignmentI al = af.getCurrentView().getAlignment();
+ seq = al.getSequenceAt(0);
}
- }
- }
- }
- // open the structure (from same PDB file or given PDBfile)
- if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
- {
- AlignFrame af = afMap.get(id);
- if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
- {
- STRUCTURE: for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
- {
- SubVal subId = new SubVal(val);
- SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
- Console.warn("Could not find sequence for argument --"
- + Arg.STRUCTURE + "=" + val);
- break STRUCTURE;
+ Console.warn("Could not find sequence for argument "
+ + Arg.STRUCTURE.argString() + "=" + val);
+ // you probably want to continue here, not break
+ // break;
+ continue;
}
File structureFile = null;
- if (subId.content != null && subId.content.length() != 0)
+ if (subVals.getContent() != null
+ && subVals.getContent().length() != 0)
{
- structureFile = new File(subId.content);
+ structureFile = new File(subVals.getContent());
Console.debug("Using structure file (from argument) '"
+ structureFile.getAbsolutePath() + "'");
}
+ // TRY THIS
+ /*
+ * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
+ * selectedSequence, true, Desktop.instance);
+ *
+ * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
+ * SequenceI[] { selectedSequence });
+ *
+ */
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
if (structureFile == null)
{
Console.warn("Not provided structure file with '" + val + "'");
- continue STRUCTURE;
+ continue;
}
if (!structureFile.exists())
{
Console.warn("Structure file '"
+ structureFile.getAbsoluteFile() + "' not found.");
- continue STRUCTURE;
+ continue;
}
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(structureFile.getAbsolutePath(),
+ DataSourceType.FILE, seq, true, Desktop.instance);
+
// open structure view
AlignmentPanel ap = af.alignPanel;
- StructureChooser.openStructureFileForSequence(ap, seq,
- structureFile);
+ if (headless)
+ {
+ Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+ StructureViewer.ViewerType.JMOL.toString());
+ }
+
+ String structureFilepath = structureFile.getAbsolutePath();
+
+ // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
+ String paeFilepath = subVals.getWithSubstitutions(argParser, id,
+ "paematrix");
+ String paeLabel = subVals.get("paelabel");
+ ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
+ af, structureFilepath);
+ if (paeFilepath == null && paeAv != null)
+ {
+ SubVals sv = paeAv.getSubVals();
+ File paeFile = new File(sv.getContent());
+
+ paeLabel = sv.get("label");
+ try
+ {
+ paeFilepath = paeFile.getCanonicalPath();
+ } catch (IOException e)
+ {
+ paeFilepath = paeFile.getAbsolutePath();
+ Console.warn("Problem with the PAE file path: '"
+ + paeFile.getPath() + "'");
+ }
+ }
+
+ // get TEMPFAC type from subvals or Arg.TEMPFAC
+ String tftString = subVals.get("tempfac");
+ TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
+ : TFType.DEFAULT;
+ ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
+ af, structureFilepath);
+ if (tftString == null && tftAv != null)
+ {
+ tftString = tftAv.getSubVals().getContent();
+ }
+ if (tftString != null)
+ {
+ // get kind of temperature factor annotation
+ try
+ {
+ tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
+ Console.debug("Obtained Temperature Factor type of '" + tft
+ + "' for structure '" + structureFilepath + "'");
+ } catch (IllegalArgumentException e)
+ {
+ // Just an error message!
+ StringBuilder sb = new StringBuilder().append("Cannot set ")
+ .append(Arg.TEMPFAC.argString()).append(" to '")
+ .append(tft)
+ .append("', ignoring. Valid values are: ");
+ Iterator<TFType> it = Arrays.stream(TFType.values())
+ .iterator();
+ while (it.hasNext())
+ {
+ sb.append(it.next().toString().toLowerCase(Locale.ROOT));
+ if (it.hasNext())
+ sb.append(", ");
+ }
+ Console.warn(sb.toString());
+ }
+ }
+
+ // TODO pass PAE label
+ StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+ false, structureFilepath, tft, paeFilepath);
}
}
}
+
+ boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
+ if (doShading)
+ {
+ AlignFrame af = afMap.get(id);
+ for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+ .findAnnotation(PDBChain.class.getName().toString()))
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+ af.alignPanel.av.getGlobalColourScheme(), 0);
+ acg.setSeqAssociated(true);
+ af.changeColour(acg);
+ Console.info("Changed colour " + acg.toString());
+ }
+ }
+
+ return theseArgsWereParsed;
}
- protected void processImages(String id)
+ protected boolean processImages(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.linkedArgs(id);
AlignFrame af = afMap.get(id);
if (af == null)
{
Console.warn("Did not have an alignment window for id=" + id);
- return;
+ return false;
}
- if (ArgParser.getValues(m, Arg.IMAGE) != null)
+ if (avm.containsArg(Arg.IMAGE))
{
- for (String val : ArgParser.getValues(m, Arg.IMAGE))
+ for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
- SubVal subVal = new SubVal(val);
+ String val = av.getValue();
+ SubVals subVal = av.getSubVals();
String type = "png"; // default
- String fileName = subVal.content;
+ String fileName = subVal.getContent();
File file = new File(fileName);
- if ("type".equals(subVal.keyName))
+ if (subVal.has("type"))
{
- type = subVal.keyValue;
+ type = subVal.get("type");
}
else if (fileName != null)
{
}
}
}
+ // for moment we disable JSON export
+ Cache.setPropsAreReadOnly(true);
+ Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
switch (type)
{
case "svg":
htmlSVG.exportHTML(fileName);
break;
default:
- Console.warn("--image type '" + type + "' not known. Ignoring");
+ Console.warn(Arg.IMAGE.argString() + " type '" + type
+ + "' not known. Ignoring");
break;
}
}
}
+ return true;
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+ private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
{
+ if (subId == null)
+ return null;
AlignmentI al = af.getCurrentView().getAlignment();
- if (-1 < subId.index && subId.index < al.getSequences().size())
+ if (subId.has("seqid"))
{
- return al.getSequenceAt(subId.index);
+ return al.findName(subId.get("seqid"));
}
- else if ("id".equals(subId.keyName))
+ else if (-1 < subId.getIndex()
+ && subId.getIndex() < al.getSequences().size())
{
- return al.findName(subId.keyValue);
+ return al.getSequenceAt(subId.getIndex());
+ }
+ return null;
+ }
+
+ // returns the first Arg value intended for the structure structFilename
+ // (in the given AlignFrame from the ArgValuesMap)
+ private ArgValue getArgAssociatedWithStructure(Arg arg, ArgValuesMap avm,
+ AlignFrame af, String structFilename)
+ {
+ if (af != null)
+ {
+ for (ArgValue av : avm.getArgValueList(arg))
+ {
+ SubVals subVals = av.getSubVals();
+ String structid = subVals.get("structid");
+ String structfile = subVals.get("structfile");
+
+ // let's find a structure
+ if (structfile == null && structid == null)
+ {
+ ArgValue likelyStructure = avm.getClosestPreviousArgValueOfArg(av,
+ Arg.STRUCTURE);
+ if (likelyStructure != null)
+ {
+ SubVals sv = likelyStructure.getSubVals();
+ if (sv != null && sv.has(ArgValues.ID))
+ {
+ structid = sv.get(ArgValues.ID);
+ }
+ else
+ {
+ structfile = likelyStructure.getValue();
+ Console.debug(
+ "##### Comparing closest previous structure argument '"
+ + structfile + "'");
+ }
+ }
+ }
+
+ if (structfile == null && structid != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ structfile = ssm.findFileForPDBId(structid);
+ }
+ }
+ if (structfile != null && structfile.equals(structFilename))
+ {
+ return av;
+ }
+ }
}
return null;
}
git://source.jalview.org / jalview.git / blobdiff