/*
* Copyright (C) 2013 SeqWare
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.seqware.common.util;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
/**
* A series of utility methods that produce human friendly output from tabbed output.
*
* Not the most efficient, since we cannot stream Strings.
*
* @author dyuen
*/
public class TabExpansionUtil {
/**
* Produce output resembling Postgres with one "table" per record
*
* @param tabSeparated
* @return
*/
public static String expansion(String tabSeparated) {
String[] lines = tabSeparated.split("\n");
// get headers
String[] header = lines[0].split("\t");
// determine maximum header length and other formatting
int maxHeader = 0;
int maxContent = 0;
for (String h : header) {
maxHeader = Math.max(maxHeader, h.length());
}
List<String[]> records = new ArrayList<>();
for (int i = 1; i < lines.length; i++) {
String[] record = lines[i].split("\t");
for (String col : record) {
maxContent = Math.max(col.length(), maxContent);
}
records.add(record);
}
maxContent++;
// do output
StringBuilder buff = new StringBuilder();
for (int i = 0; i < records.size(); i++) {
String head = "-[ RECORD " + i + " ]";
buff.append(head);
buff.append(StringUtils.repeat("-", maxHeader - head.length()));
buff.append("+");
buff.append(StringUtils.repeat("-", maxContent));
buff.append("\n");
int j = 0;
for (String col : records.get(i)) {
buff.append(header[j]);
buff.append(StringUtils.repeat(" ", maxHeader - header[j].length()));
buff.append("| ");
buff.append(col);
buff.append(StringUtils.repeat(" ", maxContent - col.length()));
buff.append("\n");
j++;
}
}
return buff.toString();
}
/**
* Produce aligned output that lines up properly in the terminal
*
* @param tabSeparated
* @return
*/
public static String aligned(String tabSeparated) {
String[] lines = tabSeparated.split("\n");
// get headers
String[] header = lines[0].split("\t");
// determine maximum header length and other formatting
int[] maxContent = new int[header.length];
List<String[]> records = new ArrayList<>();
for (String line : lines) {
String[] record = line.split("\t");
int j = 0;
for (String col : record) {
maxContent[j] = Math.max(col.length(), maxContent[j]);
j++;
}
records.add(record);
}
// do output
StringBuilder buff = new StringBuilder();
for (int i = 0; i < records.size(); i++) {
int j = 0;
for (String col : records.get(i)) {
buff.append(col);
buff.append(StringUtils.repeat(" ", Math.max(0, (maxContent[j] - col.length()))));
buff.append("|");
j++;
}
if (i == 0) {
buff.append("\n");
for (int c : maxContent) {
buff.append(StringUtils.repeat("-", c));
buff.append("+");
}
}
buff.append("\n");
}
return buff.toString();
}
public static void main(String[] args) {
String input = "Workflow Workflow Run SWID Workflow Run Status Workflow Run Create Timestamp Workflow Run Host Workflow Run Status Command Library Sample Names Library Sample SWIDs Identity Sample Names Identity Sample SWIDs Input File Meta-Types Input File SWIDs Input File Paths Output File Meta-Types Output File SWIDs Output File Paths Workflow Run Time \n"
+ "BamQC 1.0 408213 completed 2012-12-18 06:06:24.842 sqwprod.hpc.oicr.on.ca pegasus-status -l /u/seqware/pegasus-dax/sqwprod/seqware/pegasus/BamQC/run1269 CPCG_0198 305613 CPCG_0198_Pr_P_PE_354_WG 218446 application/bam,chemical/seq-na-fastq-gzip,chemical/seq-na-fastq-gzip 319329,219987,219988 /oicr/data/archive/seqware/seqware_analysis_6/sqwprod/results/seqware-0.10.0_GenomicAlignmentNovoalign-0.10.1/40527172/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R1_001.fastq.gz.annotated.bam,/oicr/data/archive/seqware/seqware_analysis_3/sqwprod/results/seqware-0.10.0_IlluminaBaseCalling-1.8.2-1/86088819/Unaligned_120530_SN1068_0090_AD0V1UACXX_2/Project_na/Sample_SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R1_001.fastq.gz,/oicr/data/archive/seqware/seqware_analysis_3/sqwprod/results/seqware-0.10.0_IlluminaBaseCalling-1.8.2-1/86088819/Unaligned_120530_SN1068_0090_AD0V1UACXX_2/Project_na/Sample_SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R2_001.fastq.gz text/json 409937 /oicr/data/archive/seqware/seqware_analysis_6/sqwprod/seqware-results/seqware-0.12.5_Workflow_Bundle_BamQC/1.0/93145099/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R1_001.fastq.gz.annotated.bam.BamQC.json 1h 50m\n"
+ "BamQC 1.0 408213 completed 2012-12-18 06:06:24.842 sqwprod.hpc.oicr.on.ca pegasus-status -l /u/seqware/pegasus-dax/sqwprod/seqware/pegasus/BamQC/run1269 CPCG_0198 305613 CPCG_0198_Pr_P_PE_354_WG 218446 application/bam,chemical/seq-na-fastq-gzip,chemical/seq-na-fastq-gzip 319329,219987,219988 /oicr/data/archive/seqware/seqware_analysis_6/sqwprod/results/seqware-0.10.0_GenomicAlignmentNovoalign-0.10.1/40527172/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R1_001.fastq.gz.annotated.bam,/oicr/data/archive/seqware/seqware_analysis_3/sqwprod/results/seqware-0.10.0_IlluminaBaseCalling-1.8.2-1/86088819/Unaligned_120530_SN1068_0090_AD0V1UACXX_2/Project_na/Sample_SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R1_001.fastq.gz,/oicr/data/archive/seqware/seqware_analysis_3/sqwprod/results/seqware-0.10.0_IlluminaBaseCalling-1.8.2-1/86088819/Unaligned_120530_SN1068_0090_AD0V1UACXX_2/Project_na/Sample_SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R2_001.fastq.gz text/json 409937 /oicr/data/archive/seqware/seqware_analysis_6/sqwprod/seqware-results/seqware-0.12.5_Workflow_Bundle_BamQC/1.0/93145099/SWID_218737_CPCG_0198_Pr_P_PE_354_WG_120530_SN1068_0090_AD0V1UACXX_NoIndex_L002_R1_001.fastq.gz.annotated.bam.BamQC.json 1h 50m ";
System.out.println(TabExpansionUtil.expansion(input));
System.out.println();
System.out.println(TabExpansionUtil.aligned(input));
}
}