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JAL-629 Commands more objecty, less classy. FileLoader with sync option (or rather...
[jalview.git]
/
src
/
jalview
/
bin
/
Commands.java
diff --git
a/src/jalview/bin/Commands.java
b/src/jalview/bin/Commands.java
index
b42f08e
..
26ce8c3
100644
(file)
--- a/
src/jalview/bin/Commands.java
+++ b/
src/jalview/bin/Commands.java
@@
-50,46
+50,65
@@
public class Commands
{
Desktop desktop;
{
Desktop desktop;
- private static boolean headless;
+ private boolean headless;
- private static ArgParser argParser;
+ private ArgParser argParser;
private Map<String, AlignFrame> afMap;
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;
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);
}
}
+ }
+
+ 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())
{
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)
{
if (id == null)
{
- cmds.processUnlinked(id);
- argsWereParsed &= cmds.wereParsed();
+ theseArgsWereParsed &= processUnlinked(id);
}
else
{
}
else
{
- cmds.processLinked(id);
- argsWereParsed &= cmds.wereParsed();
+ 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();
+
}
}
}
}
@@
-99,39
+118,31
@@
public class Commands
return true;
}
// carry on with jalview.bin.Jalview
return true;
}
// carry on with jalview.bin.Jalview
+ argsWereParsed = theseArgsWereParsed;
return argsWereParsed;
}
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)
{
{
+ boolean theseArgsWereParsed = false;
ArgValuesMap avm = argParser.linkedArgs(id);
if (avm == null)
ArgValuesMap avm = argParser.linkedArgs(id);
if (avm == null)
- return;
- else
- argsWereParsed = false;
+ return true;
/*
// script to execute after all loading is completed one way or another
/*
// script to execute after all loading is completed one way or another
@@
-157,7
+168,7
@@
public class Commands
if (openFile == null)
continue;
if (openFile == null)
continue;
- argsWereParsed = true;
+ theseArgsWereParsed = true;
if (first)
{
first = false;
if (first)
{
first = false;
@@
-353,7
+364,7
@@
public class Commands
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
- af.getCurrentView().addFile(new File(openFile), format);
+ af.getCurrentView().addFile(new File(openFile), format, false);
}
Console.debug("Command " + Arg.OPEN + " executed successfully!");
}
Console.debug("Command " + Arg.OPEN + " executed successfully!");
@@
-541,9
+552,11
@@
public class Commands
Console.info("Changed colour " + acg.toString());
}
}
Console.info("Changed colour " + acg.toString());
}
}
+
+ return theseArgsWereParsed;
}
}
- protected void processImages(String id)
+ protected boolean processImages(String id)
{
ArgValuesMap avm = argParser.linkedArgs(id);
AlignFrame af = afMap.get(id);
{
ArgValuesMap avm = argParser.linkedArgs(id);
AlignFrame af = afMap.get(id);
@@
-551,7
+564,7
@@
public class Commands
if (af == null)
{
Console.warn("Did not have an alignment window for id=" + id);
if (af == null)
{
Console.warn("Did not have an alignment window for id=" + id);
- return;
+ return false;
}
if (avm.containsArg(Arg.IMAGE))
}
if (avm.containsArg(Arg.IMAGE))
@@
-602,6
+615,7
@@
public class Commands
}
}
}
}
}
}
+ return true;
}
private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
}
private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)