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.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
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.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.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.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
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
{
headless = h;
boolean theseArgsWereParsed = false;
- if (argParser != null && argParser.linkedIds() != null)
+ if (argParser != null && argParser.getLinkedIds() != null)
{
- for (String id : argParser.linkedIds())
+ for (String id : argParser.getLinkedIds())
{
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
theseArgsWereParsed = true;
if (id == null)
{
protected boolean processLinked(String id)
{
boolean theseArgsWereParsed = false;
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
return true;
* m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
* DataSourceType protocol = null;
*/
- if (avm.containsArg(Arg.OPEN) || avm.containsArg(Arg.OPENNEW))
+ if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
long progress = -1;
boolean first = true;
boolean progressBarSet = false;
AlignFrame af;
- // 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)
+ // 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 = aav.getKey();
- ArgValue av = aav.getValue();
+ Arg a = av.getArg();
+ SubVals sv = av.getSubVals();
String openFile = av.getValue();
if (openFile == null)
continue;
}
af = afMap.get(id);
+ // When to open a new AlignFrame
if (af == null || "true".equals(av.getSubVal("new"))
- || a == Arg.OPENNEW || format == FileFormat.Jalview)
+ || 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());
+ * 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.SSANNOTATION) != null) ? m.get(Arg.SSANNOTATION).getBoolean() :
+ * (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);
* 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.argString()).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?
* (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, false);
+ 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
for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
String val = av.getValue();
- SubVals subId = av.getSubVals();
- 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
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() + "'");
}
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 = av.getSubVals();
- String paeLabel = subVals.get("label");
- File paeFile = new File(subVals.getContent());
- String paePath = null;
- try
+ // 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)
{
- paePath = paeFile.getCanonicalPath();
- } catch (IOException e)
+ 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() + "'");
+ }
+ }
+
+ // 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)
{
- paePath = paeFile.getAbsolutePath();
- Console.warn(
- "Problem with the PAE file path: '" + paePath + "'");
+ tftString = tftAv.getSubVals().getContent();
}
- String structid = subVals.get("structid");
- String structfile = subVals.get("structfile");
- String seqid = subVals.get("seqid");
- int seqindex = subVals.getIndex();
-
- // let's find a structure
- if (structfile == null && structid == null && seqid == null
- && seqindex == SubVals.NOTSET)
+ if (tftString != null)
{
- ArgValue likelyStructure = avm
- .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE);
- if (likelyStructure != null)
+ // get kind of temperature factor annotation
+ try
{
- SubVals sv = likelyStructure.getSubVals();
- if (sv != null && sv.has(ArgValues.ID))
- {
- structid = sv.get(ArgValues.ID);
- }
- else
+ 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())
{
- structfile = likelyStructure.getValue();
- Console.debug(
- "##### Using closest previous structure argument '"
- + structfile + "'");
+ sb.append(it.next().toString().toLowerCase(Locale.ROOT));
+ if (it.hasNext())
+ sb.append(", ");
}
+ Console.warn(sb.toString());
}
}
- if (structfile != null)
- {
- Console.debug("##### Attaching paeFile '" + paePath + "' to "
- + "structfile=" + structfile);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, seqindex, structfile, true, false, paeLabel);
- }
- else if (structid != null)
+ String sViewer = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
+ "viewer", null, "jmol");
+ ViewerType viewerType = null;
+ if (!"none".equals(sViewer))
{
- Console.debug("##### Attaching paeFile '" + paePath + "' to "
- + "structid=" + structid);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, seqindex, structid, true, true, paeLabel);
- }
- else if (seqid != null)
- {
- Console.debug("##### Attaching paeFile '" + paePath + "' to "
- + "seqid=" + seqid);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, seqindex, seqid, false, false, paeLabel);
- }
- else if (seqindex >= 0)
- {
- Console.debug("##### Attaching paeFile '" + paePath
- + "' to sequence index " + seqindex);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, seqindex, null, false, false, paeLabel);
- }
- for (AlignmentViewPanel ap : af.getAlignPanels())
- {
- // required to readjust the height and position of the PAE
- // annotation
- 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 boolean processImages(String id)
{
- ArgValuesMap avm = argParser.linkedArgs(id);
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
if (af == null)
}
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