/*.................................................................................................................*/ 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); } }