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.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;
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;
- public static void 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 = argparser;
+ headless = h;
+ desktop = d;
+ afMap = new HashMap<String, AlignFrame>();
+ if (argparser != null)
+ {
+ processArgs(argparser, headless);
+ }
+ }
+
+ private boolean processArgs(ArgParser argparser, boolean h)
{
- argParser = ap;
+ argParser = argparser;
headless = h;
+ boolean theseArgsWereParsed = false;
+
if (argParser != null && argParser.linkedIds() != null)
{
for (String id : argParser.linkedIds())
{
- 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);
+ }
+ }
+
}
+
}
+ if (argParser.getBool(Arg.QUIT))
+ {
+ Jalview.getInstance().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)
{
- 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 (m.get(Arg.OPEN) != null)
+ if (avm.containsArg(Arg.OPEN))
{
+ commandArgsProvided = true;
long progress = -1;
boolean first = true;
+ boolean progressBarSet = false;
AlignFrame af;
- OPEN: for (String openFile : m.get(Arg.OPEN).getValues())
+ for (ArgValue av : avm.getArgValueList(Arg.OPEN))
{
+ 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)
{
+ /*
+ * 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
- AlignmentAnnotation.TFType tempfacType = null;
- if ((m.get(Arg.NOTEMPFAC) == null
- || !m.get(Arg.NOTEMPFAC).getBoolean())
- && m.get(Arg.TEMPFAC) != null)
+ StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
+ if ((!avm.getBoolean(Arg.NOTEMPFAC))
+ && avm.containsArg(Arg.TEMPFAC))
{
try
{
- tempfacType = AlignmentAnnotation.TFType
- .valueOf(m.get(Arg.TEMPFAC).getValue()
+ 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<AlignmentAnnotation.TFType> it = Arrays
- .stream(AlignmentAnnotation.TFType.values())
+ Iterator<StructureImportSettings.TFType> it = Arrays
+ .stream(StructureImportSettings.TFType.values())
.iterator();
while (it.hasNext())
{
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
- af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
- tempfacType);
+
+ StructureImportSettings.setTemperatureFactorType(tempfacType);
+
+ af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+ format);
// wrap alignment?
- if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
+ 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 (m.get(Arg.TITLE) != null)
- af.setTitle(m.get(Arg.TITLE).getValue());
+ if (avm.containsArg(Arg.TITLE))
+ af.setTitle(avm.getValue(Arg.TITLE));
+ /* hacky approach to hiding the annotations */
// show secondary structure annotations?
- if (m.get(Arg.SSANNOTATION) != null
- && !m.get(Arg.SSANNOTATION).getBoolean())
+ if (avm.getBoolean(Arg.SSANNOTATION))
{
// do this better (annotation types?)
AlignmentUtils.showOrHideSequenceAnnotations(
}
// show temperature factor annotations?
- if (m.get(Arg.NOTEMPFAC) != null
- && m.get(Arg.NOTEMPFAC).getBoolean())
+ if (avm.getBoolean(Arg.NOTEMPFAC))
{
// do this better (annotation types?)
List<String> hideThese = new ArrayList<>();
hideThese.add("Temperature Factor");
- hideThese.add(MessageManager
- .getString("label.alphafold_reliability"));
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
AlignmentUtils.showOrHideSequenceAnnotations(
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
else
+ /* comment out hacky approach up to here and add this line:
+ if (showTemperatureFactor)
+ */
{
- if (m.get(Arg.TEMPFAC_LABEL) != null)
+ if (avm.containsArg(Arg.TEMPFAC_LABEL))
{
AlignmentAnnotation aa = AlignmentUtils
.getFirstSequenceAnnotationOfType(
af.getCurrentView().getAlignment(),
AlignmentAnnotation.LINE_GRAPH);
+ String label = avm.getValue(Arg.TEMPFAC_LABEL);
if (aa != null)
{
- aa.label = m.get(Arg.TEMPFAC_LABEL).getValue();
+ aa.label = label;
+ }
+ else
+ {
+ Console.info(
+ "Could not find annotation to apply tempfac_label '"
+ + label);
}
}
}
// store the AlignFrame for this id
afMap.put(id, af);
+
+ // is it its own structure file?
+ if (format.isStructureFile())
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
+ ssm.computeMapping(false, new SequenceI[] { seq }, 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
Console.error("Could not open any files in headless mode");
System.exit(1);
}
- }
- else
- {
- Console.warn("No more files to open");
- if (desktop != null)
- desktop.setProgressBar(null, progress);
- }
-
- }
-
- // load a pAE file if given
- if (m.get(Arg.PAEMATRIX) != null)
- {
- AlignFrame af = afMap.get(id);
- if (af != null)
- {
- for (String val : m.get(Arg.PAEMATRIX).getValues())
+ else
{
- SubId subId = new SubId(val);
- File paeFile = new File(subId.content);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subId.index,
- "id".equals(subId.keyName) ? subId.keyValue : null);
- // required to readjust the height and position of the pAE
- // annotation
- for (AlignmentViewPanel ap : af.getAlignPanels())
- {
- ap.adjustAnnotationHeight();
- }
+ Console.warn("No more files to open");
}
}
+ if (progressBarSet && desktop != null)
+ desktop.setProgressBar(null, progress);
+
}
// open the structure (from same PDB file or given PDBfile)
- if (m.get(Arg.NOSTRUCTURE) == null
- || !m.get(Arg.NOQUESTIONNAIRE).getBoolean())
+ if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
AlignFrame af = afMap.get(id);
- if (m.get(Arg.STRUCTURE) != null)
+ if (avm.containsArg(Arg.STRUCTURE))
{
- STRUCTURE: for (String val : m.get(Arg.STRUCTURE).getValues())
+ commandArgsProvided = true;
+ for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
- SubId subId = new SubId(val);
+ String val = av.getValue();
+ SubVals subId = new SubVals(val);
SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
Console.warn("Could not find sequence for argument --"
+ Arg.STRUCTURE + "=" + val);
- break STRUCTURE;
+ // you probably want to continue here, not break
+ // break;
+ 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)
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());
+ }
+
+ // 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);
}
}
}
- }
- private SequenceI getSpecifiedSequence(AlignFrame af, SubId subId)
- {
- SequenceI seq = null;
- SequenceI[] sequences = af.getCurrentView().getAlignment()
- .getSequencesArray();
- if (-1 < subId.index && subId.index < sequences.length)
- {
- seq = sequences[subId.index];
- }
- else if ("id".equals(subId.keyName))
+ // load a pAE file if given
+ if (avm.containsArg(Arg.PAEMATRIX))
{
- for (SequenceI s : sequences)
+ AlignFrame af = afMap.get(id);
+ if (af != null)
{
- if (s.getDisplayId(false).equals(subId.keyValue))
+ for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
{
- seq = s;
- break;
+ 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();
+ }
}
}
}
- return seq;
- }
- /**
- * A helper class to parse a string of the possible forms "content"
- * "[index]content", "[keyName=keyValue]content" and return the integer index,
- * the strings keyName and keyValue, and the content after the square brackets
- * (if present). Values not set will be -1 or null.
- */
- protected class SubId
- {
- protected int index = 0;
+ 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());
+ }
+ }
- protected String keyName = null;
+ return theseArgsWereParsed;
+ }
- protected String keyValue = null;
+ protected boolean processImages(String id)
+ {
+ ArgValuesMap avm = argParser.linkedArgs(id);
+ AlignFrame af = afMap.get(id);
- protected String content = null;
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return false;
+ }
- protected SubId(String item)
+ if (avm.containsArg(Arg.IMAGE))
{
- if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
+ for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
- int openBracket = item.indexOf('[');
- int closeBracket = item.indexOf(']');
- String indexString = item.substring(openBracket + 1, closeBracket);
- this.content = item.substring(closeBracket + 1);
- int equals = indexString.indexOf('=');
- if (equals > -1)
+ String val = av.getValue();
+ SubVals subVal = new SubVals(val);
+ String type = "png"; // default
+ String fileName = subVal.getContent();
+ File file = new File(fileName);
+ if (subVal.has("type"))
{
- this.keyName = indexString.substring(0, equals);
- this.keyValue = indexString.substring(equals + 1);
- this.index = -1;
+ type = subVal.get("type");
}
- else
+ else if (fileName != null)
{
- try
- {
- this.index = Integer.parseInt(indexString);
- } catch (NumberFormatException e)
+ for (String ext : new String[] { "svg", "png", "html" })
{
- Console.warn("Failed to obtain sequenced id or index from '"
- + item + "'. Setting index=0 and using content='"
- + content + "'.");
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ type = ext;
+ }
}
}
+ // for moment we disable JSON export
+ Cache.setPropsAreReadOnly(true);
+ Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
+ switch (type)
+ {
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file);
+ break;
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file);
+ break;
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName);
+ break;
+ default:
+ Console.warn("--image type '" + type + "' not known. Ignoring");
+ break;
+ }
}
- else
- {
- this.content = item;
- }
}
+ return true;
+ }
+
+ private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
+ {
+ AlignmentI al = af.getCurrentView().getAlignment();
+ if (-1 < subId.getIndex()
+ && subId.getIndex() < al.getSequences().size())
+ {
+ return al.getSequenceAt(subId.getIndex());
+ }
+ else if (subId.has("seqid"))
+ {
+ return al.findName(subId.get("seqid"));
+ }
+ return null;
}
}
git://source.jalview.org / jalview.git / blobdiff