/*.................................................................................................................*/
public void fillNameTranslation(DNAData editedData, int it, int numReads) {
Associable as = editedData.getTaxaInfo(false);
if (as == null) return;
String[] fileNames =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.origReadFileNamesRef, it);
String[] primerNames =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.primerForEachReadNamesRef, it);
String[] sampleCodes =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.sampleCodeNamesRef, it);
for (int i = 0; i < numReads; i++) {
if (fileNames == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"fileNames NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 2 + 1 < fileNames.length) {
fileNameTranslation[0][i] = fileNames[i * 2];
fileNameTranslation[1][i] = fileNames[i * 2 + 1];
} else
MesquiteMessage.warnProgrammer(
"fileNames.length too small in AceDirectoryProcess.fileNameTranslation: fileNames.length = "
+ fileNames.length
+ ", numReads: "
+ numReads);
if (primerNames == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"primerNames NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 2 + 1 < primerNames.length) fileNameTranslation[2][i] = primerNames[i * 2 + 1];
else
MesquiteMessage.warnProgrammer(
"primerNames.length too small in AceDirectoryProcess.fileNameTranslation: primerNames.length = "
+ primerNames.length
+ ", numReads: "
+ numReads);
if (sampleCodes == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"sampleCodes NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 3 + 2 < sampleCodes.length) {
fileNameTranslation[3][i] = sampleCodes[i * 3 + 1];
fileNameTranslation[4][i] = sampleCodes[i * 3 + 2];
} else
MesquiteMessage.warnProgrammer(
"sampleCodes.length too small in AceDirectoryProcess.fileNameTranslation: sampleCodes.length = "
+ sampleCodes.length
+ ", numReads: "
+ numReads);
}
}
/**
* executes a shell script at "scriptPath". If runningFilePath is not blank and not null, then
* Mesquite will create a file there that will serve as a flag to Mesquite that the script is
* running.
*/
public boolean executeInShell() {
proc = null;
try {
ShellScriptUtil.setScriptFileToBeExecutable(scriptPath);
if (!StringUtil.blank(runningFilePath)) {
if (StringUtil.blank(runningFileMessage))
MesquiteFile.putFileContents(runningFilePath, "Script running...", true);
else MesquiteFile.putFileContents(runningFilePath, runningFileMessage, true);
if (appendRemoveCommand && MesquiteFile.fileExists(runningFilePath))
MesquiteFile.appendFileContents(
scriptPath,
StringUtil.lineEnding() + ShellScriptUtil.getRemoveCommand(runningFilePath),
true); // append remove command to guarantee that the runningFile is deleted
// +StringUtil.lineEnding()+ShellScriptUtil.getExitCommand()
}
proc = ShellScriptUtil.executeScript(scriptPath, visibleTerminal);
} catch (IOException e) {
MesquiteMessage.warnProgrammer("IOException in shell script executed by " + name);
return false;
}
return true;
}