package jalview.bin;
import java.io.File;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
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.ArgValue;
+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.FileFormatException;
{
Desktop desktop;
- private static boolean headless;
+ private boolean headless;
- private static ArgParser argParser;
+ private ArgParser argParser;
private Map<String, AlignFrame> afMap;
- public static boolean processArgs(ArgParser ap, boolean h)
+ private boolean commandArgsProvided = false;
+
+ private boolean argsWereParsed = false;
+
+ public Commands(ArgParser argparser, boolean headless)
+ {
+ this(Desktop.instance, argparser, headless);
+ }
+
+ public Commands(Desktop d, ArgParser argparser, boolean h)
{
- argParser = ap;
+ argParser = argparser;
headless = h;
- boolean argsWereParsed = false;
- if (headless)
+ 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);
+ }
+ theseArgsWereParsed &= processImages(id);
+
+ // close ap
+ if (avm.getBoolean(Arg.CLOSE))
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.closeMenuItem_actionPerformed(true);
+ }
}
- cmds.processImages(id);
- argsWereParsed |= cmds.wereParsed();
+
}
}
return true;
}
// carry on with jalview.bin.Jalview
+ argsWereParsed = theseArgsWereParsed;
return argsWereParsed;
}
- boolean argsWereParsed = false;
-
- 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)
{
- 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
FileFormatI format = null;
DataSourceType protocol = null;
*/
- if (ArgParser.getArgValues(m, Arg.OPEN) != null)
+ if (avm.containsArg(Arg.OPEN))
{
+ commandArgsProvided = true;
long progress = -1;
boolean first = true;
+ boolean progressBarSet = false;
AlignFrame af;
- for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+ for (ArgValue av : avm.getArgValueList(Arg.OPEN))
{
+ String openFile = av.getValue();
if (openFile == null)
continue;
- argsWereParsed = true;
+ 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;
}
}
// get kind of temperature factor annotation
StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
- if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
- && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
+ if ((!avm.getBoolean(Arg.NOTEMPFAC))
+ && avm.containsArg(Arg.TEMPFAC))
{
try
{
- tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
- .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
+ tempfacType = StructureImportSettings.TFType
+ .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
+ .toUpperCase(Locale.ROOT));
Console.debug("Obtained Temperature Factor type of '"
+ tempfacType + "'");
} catch (IllegalArgumentException e)
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<>();
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
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)
- {
- AlignFrame af = afMap.get(id);
- if (af != null)
- {
- for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
- {
- 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())
- {
- ap.adjustAnnotationHeight();
- }
- }
- }
- }
-
// open the structure (from same PDB file or given PDBfile)
- if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
+ if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
AlignFrame af = afMap.get(id);
- if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
+ if (avm.containsArg(Arg.STRUCTURE))
{
- for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
+ commandArgsProvided = true;
+ for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
- SubVal subId = new SubVal(val);
+ String val = av.getValue();
+ SubVals subId = new SubVals(val);
SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
continue;
}
File structureFile = null;
- if (subId.content != null && subId.content.length() != 0)
+ if (subId.getContent() != null
+ && subId.getContent().length() != 0)
{
- structureFile = new File(subId.content);
+ structureFile = new File(subId.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)
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());
+ }
+
+ // 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);
}
}
}
- boolean doShading = ArgParser.getBoolean(m, Arg.TEMPFAC_SHADING);
+ // 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())
+ {
+ // 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);
+ }
+ else if (subVals.has("structid"))
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structid=" + subVals.get("structid"));
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subVals.getIndex(), subVals.get("structid"),
+ true, true);
+ }
+ else
+ {
+ 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
+ }
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+ }
+
+ boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
{
AlignFrame af = afMap.get(id);
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 = new SubVals(val);
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)
{
}
}
}
+ return true;
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+ private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
{
AlignmentI al = af.getCurrentView().getAlignment();
- if (-1 < subId.index && subId.index < al.getSequences().size())
+ if (-1 < subId.getIndex()
+ && subId.getIndex() < al.getSequences().size())
{
- return al.getSequenceAt(subId.index);
+ return al.getSequenceAt(subId.getIndex());
}
- else if ("id".equals(subId.keyName))
+ else if (subId.has("seqid"))
{
- return al.findName(subId.keyValue);
+ return al.findName(subId.get("seqid"));
}
return null;
}
git://source.jalview.org / jalview.git / blobdiff