import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import jalview.analysis.AlignmentUtils;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValue;
-import jalview.bin.ArgParser.ArgValuesMap;
-import jalview.bin.ArgParser.SubVals;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.ArgParser.Position;
+import jalview.bin.argparser.ArgValue;
+import jalview.bin.argparser.ArgValues;
+import jalview.bin.argparser.ArgValuesMap;
+import jalview.bin.argparser.SubVals;
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.gui.StructureViewer.ViewerType;
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.schemes.AnnotationColourGradient;
-import jalview.structure.StructureImportSettings;
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;
- private static boolean commandArgsProvided = false;
+ private boolean commandArgsProvided = false;
- public static boolean commandArgsProvided()
+ private boolean argsWereParsed = false;
+
+ public Commands(ArgParser argparser, boolean headless)
{
- return commandArgsProvided;
+ this(Desktop.instance, argparser, headless);
}
- public static boolean processArgs(ArgParser ap, boolean h)
+ public Commands(Desktop d, ArgParser argparser, boolean h)
{
- argParser = ap;
+ argParser = argparser;
headless = h;
- boolean argsWereParsed = true;
- if (headless)
+ desktop = d;
+ afMap = new HashMap<String, AlignFrame>();
+ if (argparser != null)
{
- System.setProperty("java.awt.headless", "true");
+ processArgs(argparser, headless);
}
+ }
- if (argParser != null && argParser.linkedIds() != null)
+ private boolean processArgs(ArgParser argparser, boolean h)
+ {
+ argParser = argparser;
+ headless = h;
+ boolean theseArgsWereParsed = false;
+
+ if (argParser != null && argParser.getLinkedIds() != null)
{
- for (String id : argParser.linkedIds())
+ for (String id : argParser.getLinkedIds())
{
- ArgValuesMap avm = argParser.linkedArgs(id);
- Commands cmds = new Commands();
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ theseArgsWereParsed = true;
if (id == null)
{
- cmds.processUnlinked(id);
- argsWereParsed &= cmds.wereParsed();
+ theseArgsWereParsed &= processUnlinked(id);
}
else
{
- cmds.processLinked(id);
- argsWereParsed &= cmds.wereParsed();
+ theseArgsWereParsed &= processLinked(id);
}
- cmds.processImages(id);
- argsWereParsed &= cmds.wereParsed();
+ theseArgsWereParsed &= processImages(id);
// close ap
if (avm.getBoolean(Arg.CLOSE))
{
- AlignFrame af = cmds.afMap.get(id);
+ AlignFrame af = afMap.get(id);
if (af != null)
{
af.closeMenuItem_actionPerformed(true);
return true;
}
// carry on with jalview.bin.Jalview
+ argsWereParsed = theseArgsWereParsed;
return argsWereParsed;
}
- boolean argsWereParsed = true; // set false as soon as an arg is found
-
- private boolean wereParsed()
- {
- 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)
{
- processLinked(id);
+ return processLinked(id);
}
- protected void processLinked(String id)
+ protected boolean processLinked(String id)
{
- ArgValuesMap avm = argParser.linkedArgs(id);
+ boolean theseArgsWereParsed = false;
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
- return;
- else
- argsWereParsed = false;
+ 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 (avm.containsArg(Arg.OPEN))
+ * // 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.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
long progress = -1;
boolean first = true;
boolean progressBarSet = false;
AlignFrame af;
- for (ArgValue av : avm.getArgValueList(Arg.OPEN))
+ // Combine the APPEND and OPEN files into one list, along with whether it
+ // was APPEND or OPEN
+ List<ArgValue> openAvList = new ArrayList<>();
+ openAvList.addAll(avm.getArgValueList(Arg.OPEN));
+ openAvList.addAll(avm.getArgValueList(Arg.APPEND));
+ // sort avlist based on av.getArgIndex()
+ Collections.sort(openAvList);
+ for (ArgValue av : openAvList)
{
+ Arg a = av.getArg();
+ SubVals sv = av.getSubVals();
String openFile = av.getValue();
if (openFile == null)
continue;
- argsWereParsed = true;
+ theseArgsWereParsed = true;
if (first)
{
first = false;
}
af = afMap.get(id);
- if (af == null)
+ // When to open a new AlignFrame
+ if (af == null || "true".equals(av.getSubVal("new"))
+ || a == Arg.OPEN || 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.SSANNOTATIONS) != null) {
+ * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean());
+ * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
+ * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
+ * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).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 ((!avm.getBoolean(Arg.NOTEMPFAC))
- && avm.containsArg(Arg.TEMPFAC))
- {
- try
- {
- tempfacType = StructureImportSettings.TFType
- .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
- .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);
+ boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.ANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
// wrap alignment?
- if (avm.getBoolean(Arg.WRAP))
- {
- af.getCurrentView().setWrapAlignment(true);
- }
+ boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
+ null, "WRAP_ALIGNMENT", false);
+ af.getCurrentView().setWrapAlignment(wrap);
// colour aligment?
- if (avm.containsArg(Arg.COLOUR))
+ String colour = ArgParser.getFromSubValArgOrPref(avm, Arg.COLOUR,
+ sv, null, "DEFAULT_COLOUR_PROT", "");
+
+ if ("" != colour)
{
- af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+ af.changeColour_actionPerformed(colour);
}
// change alignment frame title
- if (avm.containsArg(Arg.TITLE))
- af.setTitle(avm.getValue(Arg.TITLE));
+ String title = ArgParser.getFromSubValArgOrPref(avm, Arg.TITLE,
+ sv, null, null, null);
+ if (title != null)
+ af.setTitle(title);
- /* hacky approach to hiding the annotations */
// show secondary structure annotations?
- if (avm.getBoolean(Arg.SSANNOTATION))
+ boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SSANNOTATIONS, av.getSubVals(), null,
+ "STRUCT_FROM_PDB", true);
+ if (avm.getBoolean(Arg.SSANNOTATIONS))
{
- // do this better (annotation types?)
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+ /*
AlignmentUtils.showOrHideSequenceAnnotations(
af.getCurrentView().getAlignment(),
Collections.singleton("Secondary Structure"), null,
false, false);
+ */
}
// show temperature factor annotations?
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 (avm.containsArg(Arg.TEMPFAC_LABEL))
{
AlignmentAnnotation aa = AlignmentUtils
+ label);
}
}
+ */
}
// store the AlignFrame for this id
.getStructureSelectionManager(Desktop.instance);
SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
ssm.computeMapping(false, new SequenceI[] { seq }, null,
- openFile, DataSourceType.FILE, null, null, null);
+ openFile, DataSourceType.FILE, null, null, null, false);
}
}
else
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
- af.getCurrentView().addFile(new File(openFile), format);
+ DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+ FileLoader fileLoader = new FileLoader(!headless);
+ fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
+ false);
}
- Console.debug("Command " + Arg.OPEN + " executed successfully!");
+ Console.debug("Command " + Arg.APPEND + " 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
{
for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
String val = av.getValue();
- SubVals subId = new SubVals(val);
- SequenceI seq = getSpecifiedSequence(af, subId);
+ SubVals subVals = av.getSubVals();
+ SequenceI seq = getSpecifiedSequence(af, subVals);
+ if (seq == null)
+ {
+ // Could not find sequence from subId, let's assume the first
+ // sequence in the alignframe
+ AlignmentI al = af.getCurrentView().getAlignment();
+ seq = al.getSequenceAt(0);
+ }
+
if (seq == null)
{
- Console.warn("Could not find sequence for argument --"
- + Arg.STRUCTURE + "=" + val);
+ 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.getContent() != null
- && subId.getContent().length() != 0)
+ if (subVals.getContent() != null
+ && subVals.getContent().length() != 0)
{
- structureFile = new File(subId.getContent());
+ 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 });
-
+ * 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)
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
+ // ##### Does this need to happen? Follow
+ // openStructureFileForSequence() below
+ /*
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(structureFile.getAbsolutePath(),
DataSourceType.FILE, seq, true, Desktop.instance);
+ */
// open structure view
AlignmentPanel ap = af.alignPanel;
StructureViewer.ViewerType.JMOL.toString());
}
- // get tft, paeFilename, label?
- /*
- ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
- Arg.TEMPFAC);
- */
- StructureChooser.openStructureFileForSequence(null, null, ap, seq,
- false, structureFile.getAbsolutePath(), null, null); // tft,
- // paeFilename);
- }
- }
- }
+ String structureFilepath = structureFile.getAbsolutePath();
- // load a pAE file if given
- if (avm.containsArg(Arg.PAEMATRIX))
- {
- AlignFrame af = afMap.get(id);
- if (af != null)
- {
- for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
- {
- String val = av.getValue();
- SubVals subVals = ArgParser.getSubVals(val);
- File paeFile = new File(subVals.getContent());
- String paePath = null;
- try
- {
- paePath = paeFile.getCanonicalPath();
- } catch (IOException e)
- {
- paePath = paeFile.getAbsolutePath();
- Console.warn(
- "Problem with the PAE file path: '" + paePath + "'");
- }
- String structId = subVals.get("structid");
- if (subVals.notSet())
+ // 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)
{
- // take structid from pdbfilename
- }
- if (subVals.has("structfile"))
- {
- Console.info("***** Attaching paeFile '" + paePath + "' to "
- + "structfile=" + subVals.get("structfile"));
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), subVals.get("structfile"),
- true, false);
+ 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() + "'");
+ }
}
- else if (subVals.has("structid"))
+
+ // showing annotations from structure file or not
+ boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ true);
+
+ // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
+ // reference annotations
+ 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)
{
- Console.info("***** Attaching paeFile '" + paePath + "' to "
- + "structid=" + subVals.get("structid"));
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), subVals.get("structid"),
- true, true);
+ tftString = tftAv.getSubVals().getContent();
}
- else
+ if (tftString != null)
{
- Console.debug("***** Attaching paeFile '" + paePath
- + "' to sequence index " + subVals.getIndex());
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subVals.getIndex(), null, false, false);
- // required to readjust the height and position of the pAE
- // annotation
+ // 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());
+ }
}
- for (AlignmentViewPanel ap : af.getAlignPanels())
+
+ String sViewer = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
+ "viewer", null, "jmol");
+ ViewerType viewerType = null;
+ if (!"none".equals(sViewer))
{
- ap.adjustAnnotationHeight();
+ for (ViewerType v : EnumSet.allOf(ViewerType.class))
+ {
+ String name = v.name().toLowerCase(Locale.ROOT)
+ .replaceAll(" ", "");
+ if (sViewer.equals(name))
+ {
+ viewerType = v;
+ break;
+ }
+ }
}
+
+ boolean addTempFac = tft != null
+ || Cache.getDefault("ADD_TEMPFACT_ANN", false);
+
+ // TODO use ssFromStructure
+ StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+ false, structureFilepath, tft, paeFilepath, false,
+ ssFromStructure, false, viewerType);
}
}
}
+ /*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
{
Console.info("Changed colour " + acg.toString());
}
}
+ */
+
+ return theseArgsWereParsed;
}
- protected void processImages(String id)
+ protected boolean processImages(String id)
{
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
if (af == null)
{
Console.warn("Did not have an alignment window for id=" + id);
- return;
+ return false;
}
if (avm.containsArg(Arg.IMAGE))
for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
String val = av.getValue();
- SubVals subVal = new SubVals(val);
+ SubVals subVal = av.getSubVals();
String type = "png"; // default
String fileName = subVal.getContent();
File file = new File(fileName);
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, SubVals subId)
{
+ if (subId == null)
+ return null;
AlignmentI al = af.getCurrentView().getAlignment();
- if (-1 < subId.getIndex()
+ if (subId.has("seqid"))
+ {
+ return al.findName(subId.get("seqid"));
+ }
+ else if (-1 < subId.getIndex()
&& subId.getIndex() < al.getSequences().size())
{
return al.getSequenceAt(subId.getIndex());
}
- else if (subId.has("seqid"))
+ 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)
{
- return al.findName(subId.get("seqid"));
+ 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