From 3778008766299b5db71d77e8530a9c0fe9b6916d Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 17 Aug 2023 12:43:26 +0100 Subject: [PATCH] JAL-3830 JAL-4160 Remove --noheadless as --gui does this. Simplifies wrapper scripts --- help/help/html/features/clarguments-basic.html | 2 +- help/help/html/features/clarguments-reference.html | 6 +++--- help/help/html/features/clarguments.html | 2 +- help/help/icons/jalview_docs_logo.png | Bin 0 -> 11185 bytes src/jalview/bin/argparser/Arg.java | 11 +++++------ src/jalview/bin/argparser/BootstrapArgs.java | 2 +- utils/conda/jalview.sh | 18 ++++++++---------- utils/getdown/bin/jalview.sh | 14 ++++++-------- 8 files changed, 25 insertions(+), 30 deletions(-) create mode 100644 help/help/icons/jalview_docs_logo.png diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index 7a87602..e2f984f 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -409,7 +409,7 @@

- Important! If you use --output or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified --headless). To use Jalview with --output and not assume headless mode, use the --gui or --noheadless argument (the order doesn't matter). + Important! If you use --output or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified --headless). To use Jalview with --output and not assume headless mode, use the --gui argument (the order doesn't matter).

--format

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html index dd0bd52..3532af4 100644 --- a/help/help/html/features/clarguments-reference.html +++ b/help/help/html/features/clarguments-reference.html @@ -65,10 +65,10 @@ ‑‑help‑allHelp for all arguments - ‑‑headless / ‑‑noheadless - Run Jalview in headless (/ or not in headless) mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed. + ‑‑headless + Run Jalview in headless mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
- If you use a command line argument to specify an output file of some kind (--output, --image or --structureimage) then headless mode will be assumed. If you don't want this behaviour use --noheadless or --gui. + If you use a command line argument to specify an output file of some kind (--output, --image or --structureimage) then headless mode will be assumed. If you don't want this behaviour use --gui. diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index b763a81..7c2e9d5 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -163,7 +163,7 @@ If you specify an argument for an output file (one or more of --output, --image or --structureimage) then it will be assumed that you wish to run in headless mode.

- You can force Jalview to run in graphical mode using the --gui or --noheadless arguments. + You can force Jalview to run in graphical mode using the --gui argument.

diff --git a/help/help/icons/jalview_docs_logo.png b/help/help/icons/jalview_docs_logo.png new file mode 100644 index 0000000000000000000000000000000000000000..21f5386029a803303d7fff1c7c2410a354fc6dfa GIT binary patch literal 11185 zcmch72T)W`^WY=>NRlLqfPf$%Nd-ibWVl(duD<)O?q65``tGWr-t4@d?w(H5-SZ-}G?d9m7)c-qB7>KV{R3twh(DWy2eGS)u{#8jw`2ctx?Bpa!Q>?mMI#Sgmq#An58Z4aZ*Ok_duK;? ztB0;O0xoX0Y3q`V5X1_>6lC>$-mXnO_0Zc5*!|Pb3{#OK4Oe7+Ci6+a!K9wL~=L{c6zP;<_K8ki=LP4vVS{dpKxGbasM)P*yl&YpC1@h zJdcOi=!n^>LcG372AT2QJ|4I&v^)J~cjc{LX!TeBKW0iB^}BsdBbR?j6A?kPh@ zrGzFUje<$vZ{Y-|QIWbb@UlR4%oPw}1rjHio|4p+h?fcSApjHaD{+ETC`pNg41}Rg zMoXNB9jgC8<_dhQ_l(-0){=07P#j)*$mdc;Fr`%|E>upsL^@ch8>qy`N@G+6vEt%e z2V@w@aKD$skqKp`qa-Q42T{s~6X0Lwy$C5VSmLyGsNzFZ;YKp=-{S%hb~?%nrIHY3 zTQ~ulo|ha_xMPWP+@^{LX$Kq0SX6w1WD;5F2Ix!qAWB65LdQ!2DO|F|X=+o&g|q<{ z&595J!cI3pUCIPec7_vpgwf(bIZPG7rVsNVh?4Y%0RSQf|3ETamN=r8iV$QL zX4G13L<~WqY;>E%nTX&)c?g;eGYamYBY;}@DM@Fa5kiv}D=4RY25_J$cDfvTiaSu2 za`=m-j^||1(oIXYgH0Jc$d{9KWn1@yt_2%i4j#oVC`<4p)F_->vK0z$28$pH0Vqp4 z`~^`L9x1dWXvr4xCkqz}d1e%@C7A^UKVYL{r=++BvAzZ%?Rdlx(QN>-$%+ff0T4>b zU?^A%fIt*15Nl#MLG1i9JSdd0V)mh=9Te=!N+%gfcmbjm=m;VF^8g3>6k)WMl``K&=Gf z1htV#G;!8qQsKI|$lklW@7qvf5QL-7EMXUla4X;E69WjYHa>Ud)A6+?Tut{1yy9T^AJLf*sb46?oSj85Xv5K;pF)a>BEWi%56nQmv@ zRHM%L&`cR!(fW=Mf*Pm?sJ}h`d}P*dti9_ew0!ajg3z$U&vJUlHaO5y3iqoQh5J#s z5G9Q^9jW%86nu!a5Z5uF85|fjc{V{5`Q_EwL{`Md^NHdwk>?XpZ_g(pzJ#Am#Qh26qXZ%i zO{}$g2BgaR>*HlotPUQ|eLIJ|ywQmZ6enZ!l$Q>xyHD$?e3G`E;!-eg>`x{tpDMs> zOQY1;Tc-Jwvt_P{jc52;pR7k?2|};)7iTCYvJb;5h3S@ z;;$2(Pjnw#I)@O*>K87E+4rN{PDeuj-dh?l>&xQXbu>A|re?O?*D(epHkPb7=P8 z>0c`|bjdB#cW`Mu@tUXRoJks`tiVIm@v6ze6K`m#-fP~v31fWCmv%KKg~g)W_K}vzHx6dn75Y;dEnYu zmTZ$A?_r|z2BB+sVs^dANXM9!a%ri3O^H?x$JInFLGP)OxWzU7^n~K;t9J^EE~pcQ zjxUJ&@d!5UJ4V2eUn&e!UOl!~NTzAmjZdqpCeSmPEQRN)8zw(umL5mE^zA>^U}m+S zOv>ZMl8W=VrxSt5g_Em_(-7e=w+rPQ{wb#>Drks8zOh8D!Xz$S*PJjV%CT9o8?-_F zdg!;WaPO6{f0ghx&7PhQ(&Wsj$yeG-X2vDtboWQvno>ONTyj;T(uSv5XjgtgFzRx? z(F(p2JtW)0x8&sG_(UOfM)B*D+w~y8g{r#edSL22@_+TXnK=|b@x8u_T8g`_@uN3p zceS6BqB57w7Va^j=U0Lk^4l8r!ONuy(Ig>=()w>q1r(mcb(Df$`O^w_WW#LPd(W8#86QqmsjZ~v8}-@+h53-ZMx{u$@-Gx+$APWm9V zVtJ1c^5y87&60{e^0EE0B#%%Rs+&pQtqQghq+7zjF_5LwHb!VpEk?Mr)H0?Tm4u1 zwfyT~8>P*KyQ3q^ZqFC{?1L{?SF0R~{^)IyzG|bHkUztzZgI`#x46`OE;$_S?#faa zoFxSvj`-LoNJ$)DkOv#zZ*H<)P~A3AO|bR*{lz0lStf0!d~~JdV-}v@m@j1oE)MF~ zUB9Q>emVyX_9F#|`dzi$t%lQmO2D27UoRskN*k7$Bs?|uWHxlL6B%^!LD=WD@FEK; zW&z{LYqsPjA2!l#UM3o(pBMR|Z0ZzZSF?G8Uhl=+^37qs;C`2%tefbNy8`Y*{36`O zc!c#wBP~n3M|rrF3g*X+)5TF_zG$A9w;Jh2t)SNeZgk4A?}~IW`igW3`X^5U6^U(( zYWbC<>Aeh(2@g~ZE%NQ*nzvpkj%I4OO0o^D>Omz!IxcZ`^Nwpt@-_SI2_$Cbhbe;w z%cXqVD`JZs+{rd%-CrVuiktKArwCFJEy=YCCau<_44-nSTL|#`-b=kRdUszpoRTD* z!LWwKUkRB2&li&<|A+vRJ4)sVcx*hP$q~S1Mo&=5=a_|%PCt3I^=iJA77nKrbSQ^6 zOVU4rJ#pwt#8k2kKM^L{G+9I!X#gu%iR@Fm$i6pjf^c$Cn>l{fY zpABig=j*jK9@*tMjzt8vRN@^xc#p_5N#2=Bw%OT}yJ%R$UYd-yfWHiTEZ&Mh!O?<2 zY{$#S-7|;YLzE=0QoWV_@DoMkXeaN@I~%evLcU&;?^B{C$<<~^99R&;R#EW!@~J6C%ve>xxK*c>{-Ryycz)OBM-keV&yB_Oe! z_3BqU5CX@4!vmPFDsr56QSQC8y)h3wkoS;3cDgPLKd1NI%(zRzDw`b6J7A=@U_mQr zCK=K7W zvk>7UGEejL+?yv{7GMm{JN!Smns7d{Tj*qi%uvd!Xrvk8DGGKFV`E$oKN$jr3hPfN zzlmn?1%4ohTo<(ll!_Z96Gw1_Op~r#s0EWryj+z}zhEI9R%bj)1|`GRd+cPcNL>>M zn&u@YChqC!(NR)*`I6$wyZEch4rA{hGT!yC!~Pr^(#u02xW&Ybd3bnK)jkNyU%qms z{25+jbBuwydNfB-S($oub#-xBng0Fz=?;#L;87MCNs^S3vanGgh~HCE41YPQIXUCO* z;dLAWjYhK^e_iNJ(KjH&Ok_{F58q@vv1 z-GW;&cBaGxKCKvJvMfAbLMlwx|8Az6o13sr4~=?;r14mqNWxFIP+K<$nJYB1-7a2_6}Ri%tmXK zfa?iDFF=D4{&X+}nAqnP#prsCeoBp8rD!Bjr-&cs@wYcZ${!wm(@|B89JC_1Z)Wy( zYkM0@O!{PAI@#JqXS&|KpvHNsIQp`vLvJ#_!{f&uJ~}Fxl05=aI=eqVJ5!~Dn%C>* z$>#;Gmq*6Nj{fRS5P7;~U1m~UyuFTazvcDfvP~e!jy zxc;uRSNASnyjbOd(&4|~pf_{8?yYZPQd~O|XzDmp`u+DeklanLqr<5jDNZ=sVzB>+0 zm~qGP2G0`QXTgK>PvJJksS@7rSo~IR0=Zx3AZ$~@%j_S0%GWpAa^eXb+P*7>8B2ep z+@d`8?!lKv!VU9c)Yc$Y0D0dwinJI+91_=CP6GoD1~UyFKFo&0;cr=Z*z*bsR=T+| zhY~dJ79o*3O$W;*2c3d}RQC^K4j&E`Y9AaeN|$qG_{hzFj&}Eb8%|A6U$DQu=y-Cp z@B90W?aobKC`{Xn>^Y&fCYY=x|urnE*Lg?^<+r-iF@bPpNyp?vLU56>i&G-f2zu*Na{c;=Om7(L^nSS0|Dd7ZNk*0DGw;Pal?%Ksh1(1O&cwFX%m%hj^UEt6&z#%Z3s7DcIN*8+2p^;t1-8ZRRitnCUD$tN)NOB3e!l zTSkj?3(yIfN1-aNMXRfirFMpN$KOAE4gx#+cq6E#cU!WK3}m12>FH%Hhm9?RZO;ky z_4E)f{_~d^rNk|#!>Rrtkw|ozOMqHlUY_sC{$f&U>M~k|E#>XoQrnEDN?e*5L()g> z(sm$dXvBuH^nCp~G}??2SsSlbQ;uQ!KBy^OHsRd(4OP*gz|Fc0tV%Ua)MX@snhU+= z5@eddrRn9%fo{)|eU3&CYL*}n3YtXodfh|*A%d9d4Dm} z5C)5=dHf@%KM?alBi4f%WT+cq(ns0A@4h^Xpn9~oId||qHV_eTh_T<_TF{847FJ8< z)7I9GH}^$xPXAN6n=%1G)M@Pf zvodocUYFAnoM0AT^mkH$$A8g6{dZRW zd!Uy5CnO4*#2nGU00cSM% z?lEu-gEw#9%r%?dVP#{J<>%+ui2ZK6wzd`-5%I+LLa33GQyH+JPeEO<=XvzrQ+q!Q zyrlkT@Ap5$_*qBU@;`{{tUH}MrhcXWHD~5O5>iBzS6n)4tMK2l;6bj@Mi#GH4&)E@gyDvf%uU$EW_3QOOV9l~cr*WZki;t|%T5ObaCP*Y zx7pk8NY06=o6(;WGp)OIPE6F*>71B`yXW75TfpDJABDez&3osAx!*6X^0i|LT5JK(a_b%Gk9@ZHM`k zo97$$romA0KDP?;=fo~^qQ?MA%(W?BX~iBG`s{V>>J=bwG1*`kLct2$b>zUfU8&{TUI1eYHl-vHPy}W_ z8LZ`c6WHUduw2^$_C*2_0R=0tD-AXp$q-<=cb;i&QcBPry?|eTn?V3kG7}NR68qoW z4L>@`!`k0N8Ezj+fSHJ1t}PcJkhw!i!lDE)%SCH#g8N5^QZ-Z#AB!>jBG4gGOe?*6 ztWi0QU{ZgrEK;Rl@mb^W=x9l9t~|(@whoU$9hAh;`T6s8PEJL5BFIOps)VsArr33M zJ&<%4my`?-4ROF6?CiAs{2Dpz2eM?h_Wf1W)O7FNd!?hRo6aP%OhrNkE)F%oL65C( z`qCvv_bYO8T~N@_#wKrhWo3ABva~lvumn&wtd(}1l>vvg{g*g4Mv#?Ne)u5b zwK~?vDIsAB5=zi3PzaLuQGfch9?$`aQBhwW$USWP-fDva4$INl*jUNLtEeblH@C{4 z^Yh@~FGiz1Y^<%huU?hEsvM*D=utj$a8Se-Z3ogjUMZ<`&s!=)FNoy%6f!UvuXJ%w z)y~e&>pVQ)E3CS(<<8Hame_Kqtc)MAI|DMh&!3gj!SO*z&a|}U2PlX<`pU5I>z7?m zB2VgVr__A)wEXS_E=N$Qu%%P<**Q54gDSKt==7v-A>odly*=^4G1zEPe!dc157c^~ zI-A-$w6d}~!}I&M!_nR!P-N;lJHK;tcTWN-&X`f)@lGNw5&qi@9JU8dI{uA|mUEX$ z5viM39zDUV8rwX2^zt~+WoUf7xIK)*abvnk+-EcE?#Z4NHjC?spk|AGrWFwtH3)_h z?b)EH0!bMtpS-OzLPJC2jxLhAk6l-RAktgdZvj$(5IQ?LLXQJWii`C?R@LOU>!s8N z_8{40{>avrS5(xH`r5sLL>^sG#bxp6=GU=5c64-1N=~Lbk zQFxA4VM)p0Gd#j7zg=hMyZ%ODg*K0X^;NP&deAuRV1ju9YHE*Qe_wa^XJclfX2{} zU%Q9cTy=LQ$YP`Av>9yeqKIi_2)2g8iWQW!61A_?Q-yi#2sJN~xQ23Bwmr|D-94-h zIt_H1tkb?M>O7=;B>({mF8rr*2;eE*aL)9(xU{s1f{BO`tvi87KDG>x0VKVk`Gq!* z?@l1c#WG&)^T(3kxKd$%e?K5bTn;DZNdTV@D-9^2uzdlt%eU=7wSEBd>vGVSpwtY% z42*iI`EY#@)EEVdQFJ_a?=~w-)AMH!07C;wz9UGMO&Yz*Vy;NDyhOQ{f#3j&RR_S0 zNu_l}zDD}^JU@9TF4MxYk*hs-Vsf&>RD);wlU6!BZh*j zTz(GpKzw(nysN#|OhBpGq8ktp@VcPA?84>S_oC?dk(D;R9{p0gc9V5aK5uZ+%-$LO z9HJ(d4Z14W)V#rS1wAoyVxSz$LUwp>=`yHpj6Xa=VXK>V3hC01A3v@%v)E^A>FDH$ zPW#Bav>ev}T?>Fd!K}wpG%@wHC2ai^Nz1EeWaKl|)(A?&Hs5NGoFnGT3;9N_H)v8* zQ^ngKfI_e7t|QZ=J@9tly}7WR0eK4h@hW>NDiT0>__E8#Y|$Bi-9yZpyDta6tfgfR zouGLsEw6!HXCy7-?Z*t+khkl7zB@D|^Ifr^Ab^c+(9b2MrImo6eh2#A=H}+Lwj80m zVwgML%p^E+Y(4eY>6l2sVel%u)h0jJY&K#wcdL_+Dy8rr$OGI+gK!T%Q((nrHXhMh z*zZ6<8X|`?$_AqRC_9ZSb(baEwcDlMgizhfIkDGTGAT?EFA%a18+oBtvJ3rfp}4O; zv5?{s6F{yPvV)t69QhFBWc&9a=z>l|Ao(?#fwK3VawBVOO;5q+Bd<^gSQN3LoOG21 zFIV%y7bIW0H?VcIFW;|FoYbE0YqQ{zC^5A38Qv9b!A>*4#TNDAlDFEQ2-zkWAcnY5zi`ts6!(CS zqayA#JO9b!0cUc6b8K&WbWc2gjPx zcFgUfefX~pSLZ$zItiJBK0oAucK!wtB?(a^Z^e6A9VIPi*R|86lS4w;`l3QgYF@Hl zI8td$tw)Q8UtX1&Juf;@C+r7Tl`7+8ZTs5KOGV4C^gIn3d@!l81#25P&cCAK zU)sXtmDSpBtyw5wpGvTHrHK`5m+}py5!bN(j}>e6dOZvNVFQ&NeH|yzJDoP?nwXH= z_KsA@Jg7u(iaPHwhvJ5C6;{k{#5He+d$OnIZdy6sx8W1rnR(_|LD=x zu_@Afq9bnMa9Y32XL{{jl9c|z#PAfsgDPr>4doNB_fbv!Y3p^`r);uch7XMO(khaGh)N%teIRyRy_o@AA4vUFli z=EjB~`dUy|lIz%2+KpsYuZgtCxxnYhHP)pI&%5KjVSCH&hP5w~SmHER6P5+;Na@=J ztV`(36=(Q!Wd{!sIq;PpN1$h%ZO!P8IS2EU0P_T!h=rGL@pR*%CPKOSM_LzfK05-> z-cNnrc@{@W#}p%F|8SU3-Aj`gB*!mjGMv3urjCqvLN=2jr^zrkDVz=VE*;XQE+mW` z8JTS73{p>-Y(235nXYr9Q}p1C@Qq5C#5=YrXMjL3oN6ieVih{hn z(~??g7&j|Agprif50QEF<`}~*y4g9_NR`i*=-e{cd|-lDYwEOrcYEZZagRohu4!8P!4)qL|7I~aGT~DR)V`=2NCx+U+ zb>k}&-bIA;adT5|HZNhIVAD~eds+d%TF;wD{i56EJOQtS+!abb`yMj9ecn<#N>D&P z%`9PjFnC4fQti$TxHJjX9MJ3mm%HfSyKB3fVeo|ynXaVCYPzIr&#Cx%t9BzYio^tI zn{1WaE7Iru2t@O=e1Da%ZWBzZ?mt281i>-yDEiHk`==K~wpk=7U*a!jGKS2esZg_z z{0ztcF;^wb&y9m^>?8|AkZB;Uy#w6|2v&<4-ZWYdGKSqxaoR>sCjS1t5xJv&x?SNl)?xN?AIi&~Gx zR{;XS5`h%26Q%K!n1GX)CyYQU=uEZ2l-&(4j0=4FY4_cEyCC^%D_-^(Rj{$>^%VTRL&y;ja#BW$8+bRlN-O_1@Je zYvW|$8=Zl&LN|t+g*~Pp`!SQPHOO$cim}BKWbuAWS>u|IoX6nUKKY~L4-d%64&{(w z6>@Kv(Cv)imG#qhaIPvZ9GiA%q4iP8PrNCx)i*+14lc>~z)5PxKkM#`t5DlY{X=;n r%J_QGB+3|k90*$X*lNnG_u$mhUzDv_?G+N#vk**CL*bp=gOL9LLEm9_ literal 0 HcmV?d00001 diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java index 2f25978..ec915f5 100644 --- a/src/jalview/bin/argparser/Arg.java +++ b/src/jalview/bin/argparser/Arg.java @@ -29,8 +29,8 @@ public enum Arg Opt.UNARY, Opt.BOOTSTRAP), HEADLESS(Type.CONFIG, "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. " - + "Headless mode is assumed if an output file is to be generated, this can be overridden with --noheadless or --gui.", - Opt.BOOLEAN, Opt.BOOTSTRAP), + + "Headless mode is assumed if an output file is to be generated, this can be overridden with --gui.", + Opt.UNARY, Opt.BOOTSTRAP), GUI(Type.CONFIG, "Do not run Jalview in headless mode. This overrides the assumption of headless mode when an output file is to be generated.", Opt.UNARY, Opt.BOOTSTRAP), @@ -93,11 +93,10 @@ public enum Arg + "turn-propensity,\n" + "buried-index,\n" + "nucleotide,\n" + "nucleotide-ambiguity,\n" + "purine-pyrimidine,\n" + "rna-helices,\n" - + "t-coffee-scores,\n" + "sequence-id.\n" - +"\n" + + "t-coffee-scores,\n" + "sequence-id.\n" + "\n" + "Names of user defined colourschemes will also work,\n" - +"and jalview colourscheme specifications like\n" - +"--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"", + + "and jalview colourscheme specifications like\n" + + "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"", Opt.STRING, Opt.LINKED, Opt.ALLOWALL), FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.", Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java index 4b7b180..f51e4c5 100644 --- a/src/jalview/bin/argparser/BootstrapArgs.java +++ b/src/jalview/bin/argparser/BootstrapArgs.java @@ -362,7 +362,7 @@ public class BootstrapArgs } else if (this.contains(Arg.HEADLESS)) { - // --headless, --noheadless specified => use value + // --headless has been specified on the command line => headless isHeadless = this.getBoolean(Arg.HEADLESS); } else if (this.argsHaveOption(Opt.OUTPUTFILE)) diff --git a/utils/conda/jalview.sh b/utils/conda/jalview.sh index c9ec026..995195f 100755 --- a/utils/conda/jalview.sh +++ b/utils/conda/jalview.sh @@ -66,21 +66,19 @@ HEADLESS=0 GUI=0 HELP=0 DEBUG=0 -for ARG in "${@}"; do +for RAWARG in "${@}"; do + ARG="${RAWARG%%=*}" case "${ARG}" in - "--headless") + --headless|--output|--image|--structureimage) HEADLESS=1 ;; - "--help") + --help|--help-*|--version) HELP=1 ;; - --help-*) - HELP=1 - ;; - "--gui") + --gui) GUI=1 ;; - "--debug") + --debug) DEBUG=1 ;; esac @@ -174,7 +172,7 @@ fi JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" ) if [ "${DEBUG}" = 1 ]; then - echo Shell running: "${JAVA}" "${JVMARGS[@]}" -jar \""${JARPATH}"\" jalview.bin.Launcher "${ARGS[@]}" + echo Shell running: "${JAVA}" "${JVMARGS[@]}" -jar \""${JARPATH}"\" "${ARGS[@]}" fi -"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" jalview.bin.Launcher "${ARGS[@]}" +"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" "${ARGS[@]}" diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh index 371bfcd..9281be2 100755 --- a/utils/getdown/bin/jalview.sh +++ b/utils/getdown/bin/jalview.sh @@ -41,21 +41,19 @@ HEADLESS=0 GUI=0 HELP=0 DEBUG=0 -for ARG in "${@}"; do +for RAWARG in "${@}"; do + ARG="${RAWARG%%=*}" case "${ARG}" in - "--headless") + --headless|--output|--image|--structureimage) HEADLESS=1 ;; - "--help") + --help|--help-*|--version) HELP=1 ;; - --help-*) - HELP=1 - ;; - "--gui") + --gui) GUI=1 ;; - "--debug") + --debug) DEBUG=1 ;; esac -- 1.7.10.2